Midnight Blue Eyes

Her eyes say you shouldn't mess with her.

Midnight Blue Eyes are a subtype of Blue Eyes that have their own sets of connotations. Some of these have some intersection with Icy Blue Eyes, Green Eyes, and Gray Eyes. Physically, Midnight Blue Eyes appear to be a dark, intense shade of blue, although blue-black variations (also with an intense look) also count. These eyes are typically seen in heroic characters or in type 2 or 3 antiheroes. The connotations are as follows.

Like Icy Blue Eyes, these eyes seem to pierce through you.
Characters with these eyes tend to be very combat orientated. A common hue for the Badass.
Tend to be aloof or a lone wolf. Sometimes cold, much like Gray Eyes.
Generally meaner, more cynical, and not as naive when compared to Innocent Blue Eyes.
Elemental powers are relatively unpredictable, being any element associated with a storm, such as water (includes ice), wind (like Green Eyes), or lightning (like Eyes of Gold).
Danger. Not in the sense of malice, but in that provoking/pissing off a character with these eyes is not very wise, as they will most likely pummel you if you do. Bottom end of Uh-Oh Eyes for this reason.

Related to Icy Blue Eyes, Gray Eyes, and Green Eyes due to similar connotations. Most benevolent type of Uh-Oh Eyes, as explained above.

No real life examples, please; Even if eye color had a meaning in Real Life, so many people have blue eyes that we'd be here all day.

Examples of Midnight Blue Eyes include:

Anime and Manga

The Blue Eyes White Dragon from Yu-Gi-Oh has very dark blue eyes. In ancient Egypt, the beast was a creature of good, albeit a very violent and destructive one. The Millennium Arc explains Kaiba's connections with the dragon.
- Kaiba himself, who is one of the nastier examples of this trope. Kisara's eyes act as a Chekhov's Gun (see above). Ishizu's eyes are dark blue. She's also a Lady of War.
Ranma Saotome of the Ranma ½ anime has this type of eyes. He's one of the best, most adaptive fighters in a cast full of martial artists, so he fits into the Badass territory.
Shinji Ikari and his father Gendo from Neon Genesis Evangelion have these, both of them being serious, aloof and definitely not the sort of people you want to piss off. Although in Shinji's case it also overlaps with Innocent Blue Eyes.
L from "Death Note" gets these as part of his expressive Inner Monologues in the anime. It's used in contrast with Light's dangerous red eyes.

Comic Books

Batman. Also Tim Drake, Dick Grayson, Damian Wayne... most of the Batfamily, really.

Literature

Thalia Grace from Percy Jackson and The Olympians fits most of the criteria above. She's a Snark Knight who's very skilled at fighting monsters with her lightning-based powers.

Tabletop Games

Bahamut's eyes change from Innocent Blue Eyes to Midnight Blue depending on his mood (when he gets mad) in Dungeons & Dragons. You're screwed if you're the reason they changed as he intentionally invokes Mugging the Monster on people.

Video Games

Both Adell and Yukimaru (pictured above) in Disgaea 2: Cursed Memories have dark blue eyes. Both are capable warriors. The former is so dangerous that he drove out most of the demons from Veldime in Disgaea 4: A Promise Unforgotten, while the latter has ice powers. Both are also examples of Uh-Oh Eyes as they're both demons, especially Yukimaru, as there's other things abnormal about her eyes due to a Snow Clan trait.
- Archers (female) are commonly depicted as having dark blue eyes. It fits, considering that they have strong bonds with wind spirits and bow attacks often deal water damage.
Zero invokes most of the connotations of the trope in Mega Man X, including elements via special attacks. Compare with Ciel's Innocent Blue Eyes.
- Craft is a rare evil example in Mega Man Zero.
Falco's eyes are dark blue in Star Fox. One of the stronger pilots and very aloof to boot.
Gwendolyn from Odin Sphere has dark blue eyes. Is also a Badass Princess with a powerful psypher.

Western Animation

Although most of the cast of Phineas and Ferb have dark blue eyes (except for Jeremy, who has light blue eyes, and Perry the Platypus, who has light brown eyes), the only ones that actually fit for the purpose of Midnight Blue Eyes are Isabella, Isabella-2, and Candace-2, and that's due to Badass tendencies.