Personally, the only one that came close to getting a major nomination it did not receive is The Dark Knight. But if I could nominate a few more out of preference?
The Dark Knight: Best Picture, Best Director, Best Adapted Screenplay, maybe Best Actor (I'd have to go back and see how competitive the year was, I just remember Sean Penn deservedly winning for Milk).
Logan: Best Picture, Best Supporting Actor (then again Michael Stuhlbarg should have been nominated for Call Me by Your Name so it's a tough year), maybe Best Actor.
Spider-Man 2: Best Adapted Screenplay, I want to say Raimi for Best Director, because I think his work was better than Taylor Hacker and Mike Leigh who were both nominated, but that just tells me the Academy probably missed some great choices that year who were better than Raimi too.
The Dark Knight Rises: I'm tempted to say Best Picture, because it sure as hell was better than the film version of Les Miserables (and I LOVE the show), but you know I could make that argument for Flight, The Master, Seven Psychopaths, and even arguably Skyfall that year, so... I'd also be amused if Tom Hardy received a Best Supporting Actor nomination... but I honestly can't say he is better than the five who got nominated, so probably not.
For major awards that's about it. But I'll throw in Michelle Pfeiffer for Best Supporting Actress in 1992 for Batman Returns. That was a phenomenal performance, even if I don't really think it was Catwoman or Oscar-y.