Special Effect Branding

In the real world, things which serve the same purpose tend to have similar form factors: different brands of car do look different, but they're all recognizably automotive. Different models and brand of tank, plane, or gun all look different, but are still similar enough that someone not well-versed in the particulars would still be able to identify them at first glance.

Not so in Science Fiction: If two different races have similar technology, it must look radically different, even in the visual effects they use. One might think that Energy Weapons based on the same physical principles would give off a visual effect characteristic of that principle, so any weapon that works in the same way would look the same -- not so. In fact, each weapon will reflect the race of its builder. This might seem doubly strange as the aliens themselves tend to all look exactly like humans with a funny nose glued on. The realm of Special Effects is the one place where show designers seem to remember that the product of alien development should look really radically different from Earth development -- even though it's an area where one would expect form to follow function. Two species will not use the same special effects for the same technology, unless a point is being made that they are trading science (and not always then). Perhaps there's an intergalactic trademark office which registers the colors of laser beams. Lasers, incidentally, can be made any color but because the different wavelengths behave differently colors would probably end up distributed by the task the weapon was designed for rather than by species.

Note that this specialization is a comparatively recent phenomenon: In bygone days when budgets were lower, effects were harder and audiences cared less, everyone used the same film-negative effect for lasers, and the same V-2 spaceship design.

It's also worth noting that characters in these series almost never notice this: there are plenty of episodes of the various Star Trek series where characters are ambushed with weapons fire being distinctively e.g. Klingon, yet they won't figure out that it's the Klingons until they can see them themselves.

Specific form of Color Coded for Your Convenience.

Anime and Manga

 * In the 2003 anime adaptation of Fullmetal Alchemist, the Transmutation circles vary depending on what's being transmuted, whether the alchemist has seen the Gate, and other factors.
 * Justified; different circles are designed to do different things.
 * In Fullmetal Alchemist: Brotherhood, the sparks from alchemy use are normally blue, but when homunculi regenerate or someone uses a Philosopher's Stone, they're red.

Film

 * In Star Wars, Red lightsabers are Evil, Blue and Green are Good. Purple ones are apparently reserved for badass motherfuckers.
 * Averted in at least one Expanded Universe story, in which Leia's lightsaber is red. Corran Horn also manages to create a lightsaber that can do two different colours depending whether it's set to its regular length or an Awesome but Impractical setting that turns it into a BFS.
 * A separate Star Wars example is the colour of blaster and turbolaser weapons. In the original trilogy, this trope was used in the space battle scenes (where the Empire used green and the Rebels used red, an interesting reverse of the usual lightsabre colour branding) but was not used in ground fights, where all bolts were red. The prequel trilogy on the other hand used it for ground battles as well, the Naboo using green, the Trade Federation using red and the Republic using blue (confusing some Expanded Universe fans who were used to the games colouring ion-cannon fire blue.
 * In the Harry Potter films, Death Eaters and Order members have different Apparating effects for no reason. Death Eaters turn into menacing clouds of smoke while Order members turn into blazes of white light. It looks rather cool, though.
 * Rather cool being an understatement.
 * Not to mention that the (Slytherin to a man) villains tend to use a lot of green Avada Kedavra spells, while the (almost entirely Gryffindor) heroes stick to red Expelliarmus and Stupefy spells.
 * Your Mileage May Vary on that. Having the Mooks do anything makes it less cool.

Live Action TV

 * Doctor Who: Whatever may have happened in the old days, "The Christmas Invasion" raised some loud arguments in fandom because the Sycorax and "Pilotfish" used the same visual effect for their teleports. The plot thickened somewhat when the "pilotfish" returned for "The Runaway Bride" and were revealed to have nothing whatever to do with the Sycorax.
 * Also, there was a spoiler for Doomsday in the trailer for Army of Ghosts: a brief clip of action from the second episode was inserted instead, and it contained.
 * In modern-era Star Trek, each race has its own set of special effects: red phasers and blue transporters for Star Fleet, red transporters and green phasers for Klingons, and so forth. Star Trek: Deep Space Nine made a special point of this, as the titular station, though operated by Star Fleet, was of Cardassian origin and used Cardassian effects. In the original series, everyone used more or less the same visual effects, and the Romulans and Klingons even shared a ship design. (This was explained on screen as the result of their collaboration. Off screen, they had broken the original Romulan ship model.)
 * However, the original series does have one example of this. In "Mirror, Mirror", the transporter chamber on the evil Enterprise uses a different beaming effect than the one on the good Enterprise.
 * Also, while most Aliens have their own ship designs, all the races inside the Federation use the same basic design for their ships. In Enterprise (which takes place before the Federation was founded) all future Federation members (Vulcans, Andorians, humans,...) now have radically different ships, with human ships most closly resembling future Star Fleet design.
 * One glaring example may be the Ferengi phaser whips used in their original appearance. While most personal phasers and disruptors resemble pistols or rifles, the Ferengi built phasers in the shape of tubes that fire when uncoiled in the direction of the target.
 * Stargate SG-1 gives each major player their own radically different ship design and weapon effects, ranging from Egyptian pyramids to Earth naval ships to bioships, though there is an exception: the minor races all use the same (Goa'uld) design of ship, having acquired them second hand. That said, the technology of both humans and aliens in the Pegasus Galaxy of Stargate Atlantis looks quite different. Even the gates are of a different design. And despite their obvious usefulness, the Atlantis team does not appear to have brought any Zat guns or staff weapons with them, nor have they sent any Wraith stunners or (with one temporary exception) puddle jumpers back home.
 * That puddle jumper was already found in Milky Way. It was built by Janus after leaving Atlantis.
 * Babylon 5: Ships from every power look far different from each other, and even their propulsion systems and weapons are different. The Minbari build ship with giant fins and no visible engine that fire beam weapons, the Centauri love fins and wings, but they have visible, glowing thrusters. They use beam and projectile (plasma?) weapons, and can generate internal gravity. The Narn paint their ships with geometrical designs, and are powered with big thrusters. They like wedge-shaped ships with mandible-like extensions, even their fighters look that way. Human ships are in general boxy, and use rotating sections for gravity. Earlier ships are painted blue, later ships have drab-military colors. All their ships have thrusters that glow blue, except the new Starfury fighters which have thrusters that glow red (for no apparent reason.) They use red lasers and plasma weapons that change in color, generally by size: small are bluish, big are greenish. The Drazi have winged ships with odd, bulbous engines that don't seem to be thrusters. The Shadow ships don't look like ships at all: "Spiders black as death and twice as ugly." They fire blue beams that are very distinctive and unique: no one else has blue beam weapons. Vorlon ships are all curves and no straight lines with dappled shifting skins. They range from green to red in color, with dark spots. They seem to use thrusters, but have also expanding flower-like petals with shifting colors. Their weapons are fired from forward tentacles and phased together (Death Star style) One episode explains that the wavelength of laser depended on the materials used in construction, and therefore the race could be identified knowing the wavelength of the lasers used. However, we see several times mixed-design ships:
 * The White Star ships: Minbari-Vorlon: Minbari-style fins with Vorlon-style dappled organic armor. They use a main beam weapon similar to Minbari ships, and discreet plasma bolts.
 * The Advanced Destroyers: Earth ships that had been adapted with Shadow tech. Their outward appearance was the usual boxy utilitarian shape (with a few spines added) but the hull had the black, shifting appearance of the Shadow vessel skin. They also fired the blue beams.
 * The Valen: In Legend of the Rangers: To Live and Die in Starlight a Minbari-Earth combined design: boxy like a human ship fitted with the non-thruster type Minbari propulsion.
 * The Valen-class ship in The Lost Tales appears to be a redesign and looks distinctly Minbari.
 * The Excalibur and Victory: In A Call to Arms we are introduced to what is supposed to be a White Star scaled to destroyer size. They have three big wings/pylons and a bulbous front end with multiple beam canons. They have flat gray armor (non-organic) but the main weapon is fired from the pylons and phases like a Vorlon weapon.
 * It is an adapted Vorlon weapon. The reason for the 1 minute power outage is because they can't replicate the Vorlon power source (some fan material claims they tap hyperspace directly).
 * Both used and subverted throughout Firefly and Serenity. The Alliance and civilian vessels (particularly Serenity) have very distinctive differences from each other. However, while definitely "branded" with their Spikes of Villainy, painted blood, and corpses, the Reaver ships are still recognizable by class - one shot from Serenity's fleet battle shows an Alliance frigate and a Reaverized counterpart of the same ship in great detail.

Video Games

 * In the Descent: Freespace series, apart from the fact they all use engines, lasers and subspace drives, It's hard to tell that Terran, Vasudan and Shivan ships are even from the same universe.
 * Terran vessels are boxy, grey and decidedly 'military' in aspect to reflect their 'utilitarian' attitude (this is practically a trope in itself). In Freespace 2 they become more streamlined due to tech-sharing and Vasudan influence, although this process doesn't seem to work in reverse.
 * The early Vasudan ships, especially freighters such as the Bast and Ma'at classes, are as clunky and boxy as their Terran equivalents, but they seem to have crossed the starship Bishonen Line much faster than the Terrans. Even the Shivans are going this way, from the harsh, severe, jagged asymmetrical contraptions of the first game to the insectile designs of the second.
 * Vasudan ships look vaguely like alien creatures, particularly beetles. According to the Tech Room, they are based off creatures that live on the planet Vasuda, supposedly because of their highly philosophical culture.
 * The Shivans... well their ships are painted black, red and silver and fire off red lasers. They also have the tendency to have random spikes sticking out, and be asymmetrical with an off-center engine. God knows how Shivans manage to balance their ships. Maybe that's why the captured Terran-modified asymmetric Dragon in FS1 was crippled, while the captured (symmetrical) Mara you flew in FS2 was awesome. But I digress. This, of course, shows that the Shivans are just plain weird (and evil).
 * Space is not an ocean. They wouldn't need to have their ships balanced; the engine placement has no effect, aside from pointing where the craft is going.
 * Incorrect. An off-center engine would impart rotational force on the ship whether on water or in space--in fact, this is the principle behind the maneuvering system of any practical spacecraft--numerous small thrusters distributed at specific points on the craft to turn it on any axis desired. A Nephilim-class bomber ought to spin like a top with its main thruster off to one side.
 * Used in Eve Online. The Amarr have sleek, symmetrical, shiny golden ships with beam weapons. The Gallente have smooth-shaped, almost organic-looking green ships with Attack Drones and blasters. The Caldari have utilitarian, gunmetal grey/blue, angular ships with railguns and missiles. The Minmatar have rust-brown/red heaps'o'junk which fly at unsafe speeds and the larger ships fire car-sized artillery shells. Some of the minor factions also have their own designs. Angel Cartel fly ships that resemble the Shivans mentioned above, the Sansha ships look like they have been designed by a sadomasochist, the rogue drones are basically mechanical insects and the Jove fly Gigeresque biomechanical ships.
 * In Sins of a Solar Empire, the three sides have different ship designs and different weapons. Even weapons that are supposed to be similar between the sides have different effects. Most of the TEC ships are hastily-converted cargo haulers and passenger liners, and it shows. The Kol-class battleships are the only ones that were designed specifically for war, but their appearance is decidedly utilitarian. They primarily use pulsed lasers and kinetic weapons. The Kol is equipped with powerful red laser beams. The Advent are psychic cyborg humans whose ships feature sleek, gleaming designs. Their staple weapons are bright blue beams that look nothing like the TEC lasers. The Vasari, being nonhuman, feature vastly different designs, although not different enough not to be recognizable. They're still sleek, but alien sleek. Their weapons are mostly of the green plasma variety.
 * Star Control II has a wide range of Starfish Aliens and Rubber Forehead Aliens, with ships designed to meet their physiological needs as well as using their unique weapons systems. While you may control ships designed by a specific race, you must also have pilots of that race to control them.
 * Sword of the Stars averts this trope in that all factions have similar effects for their weapons, and weapons effects in fact represent the technology level and type of the weapon - green lasers for example, used by anyone, are stronger than red lasers used by anyone. While each faction's ships do, however, look drastically different from the other factions' ships, the game does provide varying degrees of technological or cultural justification for this, including the fact that each faction has a different stardrive from the others around which they base their ships.
 * Champions Online uses this trope where it can - the ships of the alien enemy Qulaar are insectile and highly organic, while the ships of the froglike Gadroon are sleek, shiny, have no visible engine or thruster, and apparantly Bigger on the Inside - a cruiser large enough for a full terraforming force with dozens of Gadroon is barely half again larger than an F-22. On the other hand, player characters have a huge variety of armor, weapon, and even jetpack styles to choose from, and many will mix and match.

Western Animation

 * Taken to an extreme in most Transformers series, where everybody's weapons are theirs and theirs alone. This is a combination of the Merchandise-Driven idea of making sure everyone uses the weapon they come with and launches the appropriate missiles, and the fact that, as Transforming Mecha, their weapons are more or less part of them.
 * This doesn't explain why ships tend to have similar variety, though.
 * Actually averted in one of the G1 animated episodes. The Decepticons have captured the Autobots with the exception of Wheeljack. Wheeljack manages to infiltrate their holding cell, discovers his buddies are tied up, depowered, soaking wet (bad thing for robots), and with their carbine-shaped weapons piled sloppily in the corner. He then proceeds to go Guns Akimbo--pointing AT THE AUTOBOTS. "My friend's weapons! Hmm. Okay, Sideswipe's flare gun should dry off your circuits, and Bluestreak's bolts should give you all an instant recharge!" It's amazing the first thing Optimus didn't do was Face Palm: "It's a wonder the Decepticons didn't just kill us outright, but vector sigma, am I the only one that knows that guns are supposed to be for killing?"
 * Additionally, in some continuities, each faction has different colored beams from their energy weapons. The different factions also generally have different coloured eyes (blue for Autobots, red for Decepticons) although their optical sensors presumably all function the same way.
 * Beast Wars averts this. While all the characters do have their own signature weapons, the Maximals have a separate armory, supposedly for gunless characters like Dinobot.