Moon/WMG

The first Sam we see is simply having a Dying Dream; none of the movie actually happened.
First Sam We See (henseforth called FSWS) crashes into something, and spends some time slowly dying in the rover. And at the climax of the film, he's put back into said rover in order to complete the illusion. But can we trust the perception of a man slowly dying? ''FSWS didn't go anywhere. The last time he moved his head was to imagine seeing a healthy, virile version of himself going home''. The entire film is spent in a few moments of FSWS's brain misfiring.
 * This would be an intensely disappointing ending, but it seems plausible as an option.

The clones don't have a three-year "termination date".
"Old" Sam's symptoms are those of radiation poisoning: vomiting blood, losing teeth and hair, and so forth. The clones aren't designed to self-destruct; rather, despite the shielding on the base, constant cumulative radiation exposure results in a lethal dose after about three years. "Young" Sam may just live a normal lifespan on Earth.
 * Possible but doubtful. We know that if Sam Zero actually did his three years, he survived them.

Sam dies in the end.
Simply put, the He3 launch is not designed for human passengers. It's designed to decelerate appropriately for a solid stable cargo. This would kill a human. Furthermore the recovery team that picks it up in the ocean would pop it open and see Sam, and the company man on board would have him destroyed and the crew forbidden from speaking of it. Or perhaps the ship sunk with all hands lost.
 * There's some radio chatter in the end that says "Lunar's stock has slipped 30-32%..." and "The clone of Sam Bell has been giving evidence at CEA's board of directors in Seattle". So, he lives. Now, Lunar may have killed the new clone in the base unless he used the jamming tower's destruction to contact Earth.
 * The line is "Clone six, the clone of Sam Bell has been giving evidence...". The director's commentary tells us old Sam and new Sam are Sam-five and Sam-six respectively, something you can also work out from Eve's age assuming the original was Sam-one. Thus, the Sam that went through the He3 launch very definitely survived.

Earth is dead.
The AI includes a small amount of intrigue and fun, because it's bored. It sets up fake conversations with Earth and the two corporate suits. This is why the "realtime" communication between them is instantaneous rather than with a few-seconds delay from Earth to Moon. The radio chatter heard at the end when Sam goes to Earth in the He3 launch is a hallucination or a dream.

Earth is dead and empty, and the Moon base has been mining He3 for centuries after without pause. The He3 launch lands in the ocean and eventually washes ashore, containing a deceleration-slain Sam, and there is nobody around to find it.


 * Not to mention the line from Gertie "I hope Earth is as you remember it."
 * Set to be Jossed -- there's going to be a sequel, Mute, set in Berlin.

Gerty loves Sam.
Even if he was programmed to care for Sam, he went far and above in Sam's defense over the company's interests, despite having to keep up the pretense of normalcy. The sympathetic hand (well, robotic clamp) and teary smiley face just go to show how much an emotionless monotone can mask a 24 karabyte heart. "Sam: Are you sure you want me to do this? It will wipe your entire memory!
 * This Troper agrees. I was actually expecting a scene like this:

Gerty: My primary function is to help you, Sam.

Sam: But...

Gerty: Sam?

Sam: Yes, Gerty?

Gerty: I love you.

Awkward silence.

Sam: Okay, lets wipe that memory of yours now."


 * Thirded, I was quite surprised to notice myself expecting an "I Love You, Robot Buddy!" moment...
 * When Isaac Asimov first saw 2001: A Space Odyssey, he noted that HAL obviously wasn't programmed with the First Law of Robotics. Perhaps GERTY was -- and more to the point, he may have been programmed to think of the clones as not qualifying as human, but he changed the definition after Sam began discovering the truth. GERTY also has the advantage that when the secret he was supposed to keep from his crew started to unravel, he simply came clean, instead of trying to pull off a tragic Fawlty Towers Plot like HAL did.

Sam loves GERTY
Put away your Fetish Fuel, I mean he loves GERTY in a familial or platonic way. Beyond the affection he shows for GERTY overall in the movie, there's also the line where GERTY is talking about being programmed and Sam says "We're not programs, GERTY, we're people!". If you take this "We" to be not just the clones but the clones and GERTY...(which I did on viewing the film)...

Sam really did go to the moon
Sam was shipped to the moon, did his three years, and returned home. The video links between Sam-clone and his wife were the REAL video links between Sam and his wife, but with any details that didn't add up blocked due to "disturbance". The wooden town took approximately 15 years to build (GERTY gives the exact amount of hours, which comes out at about this), which would allow Eve time to grow up. Once his 3 years were up, he returned home, and the Sam clones were built/shipped in. This was probably done without his consent. The Sam we see was probably the 4th or 5th generation clone since the original Sam was sent up.
 * This isn't a Wild Mass Guess; it's true. Word of God confirms that the original Sam Bell did in fact spend three years on the moon and then return home - that's where they got the memories for the Sam clones. You can hear him offscreen when Sam calls his daughter near the end.
 * The real question is: was the original Sam ("Sam Prime") party to the cloning plot? Or an unwilling dupe?
 * It seems likely that it played out this way: Sam Prime signs up for his three-year hitch at Sarang. No mention of cloning has been made to him, but deep in the contracts he signed with Lunar Industries are the rights to use his genome in whatever way they see fit. When he arrives at the base, he gets settled, learns everything he needs to know to work there, makes friends with Gerty, etc. Then he's sent out in a rover to see what's the matter with the mining machine "Luke" (which may not even actually exist). He never makes it. He is drugged (possibly before he even makes it to the rover). Gerty watches over him while a crew from Lunar Industries arrives to sample his genome, scan his memories, and install both in the "nursery," the hardware for which is already part of the base, lacking only DNA and a memory scan to function. Sam Prime wakes up in the infirmary just as we've seen the clones do, is told he was in a rover crash, then recovers and serves the rest of his three-year hitch. The "return vehicle" room is hidden from him behind a bulkhead; when it's time for Sam Prime to go home, a ship comes to pick him up. He returns home and lives out his life, thinking someone else arrived to take over the base after he left. Meanwhile, the clones have been growing in the nursery. After Sam Prime leaves, Sam-1 awakens in the infirmary, and is told he was in a rover crash...

The Co-ordinates of the Harvesters Are Bible Verses.
But I'm too lazy to go and check.

Sam murdered his wife
When Sam is talking to Eve she tells him with a suspiciously ominous tone that her mother had died and seem fearfully of her father when he comes to the phone. Also when sam is first awaken he clearly has a problem controlling his temper and is shown later to be perfectly willing to sacrifice a clone of himself for his own benefit. Assuming than his original personality was similar it's seems more than likely than he was a willing accomplice to the cloning plan. When his wife found out what he had done she threatened to spill the beans causing him to snap and killed her.
 * Seems pretty Jossed near the end of the film, though. Sam 2 has the opportunity to revive a new clone and kill him to trick the rescue team. However, Sam 1 calls 2 out on it, saying that he knows 2 is unable to kill another person because he himself can't either.
 * Also, bear in mind that Eve is talking to a guy that talks and sounds EXACTLY like her father (albeit a younger version), while knowing that her dad is in the same house. She's not being ominous, she's just fucking baffled.

Christian Bale and Sam Rockwell are increasingly degraded clones of Tom Cruise.
Okay, I'm kidding.
 * But that explains everything!
 * But then how does Sam Rockwell have the voice of Owen Wilson?

Gertie has been slowly evolving to be more human.

 * Gertie has been gradually acquiring a more human personality over the course of his "life." Not a very exciting wild mass guess, but it seems like an appealing idea. When the mission first began, Gertie started out as just a simple, mindless, emotionless robot, without any tendency to care for Sam beyond what his programming demands. However, by the time the events of the movie occur, Gertie himself has been on the moon with no-one but the Sam clones for company for many, many years. Gertie, after all, isn't replaced every 3 years... He's had to live through it all for all this time. Gradually and slowly, he's been growing beyond his original programming, the conflict of watching each successive Sam die wearing on him, something like regret and other emotions slowly evolving; and so by the time of the film, he's almost a full-fledged Ridiculously Human Robot. That may be part of the reason why in the film, he (gradually) becomes willing to reveal the truth to the Sam clones, but why it seems he's never done so before.

The whole movie is one giant Batman Gambit

 * One of the higher-ups at Lunar Industries starts feeling guilty about killing clone after clone OR
 * Sam-Prime finds out about the clones aboard the lunar base, and decides to expose them for what they are: criminals, by orchestrating the whole film. Sam-Prime, working either solo or with some sort of a mole at Lunar Industries, contacts GERTY, and, using their previous friendship, convinces GERTY to aid them in exposing Lunar Industries.