My personal favorites are
1.) The Dark Knight
2.) Batman Begins
3.) Batman '89
4.) X2: X-Men 2
5.) The Watchmen
6.) Dick Tracy
7.) X-Men: Days of Future Past
7.) Deadpool
8.) Unbreakable
9.) Superman (Donner)
10.) Spider-Man 2
11.) Hellboy
12.) Iron Man
13.) Guardians of the Galaxy
14.) Superman II
15.) Blade 2
Honorable Mention: Fantastic Four: Rise of the Silver Surfer (I dunno I feel like the two FF movies before the reboot are not so bad and feel more like a Marvel Comic to me).
As you can tell ... while I can enjoy the Marvel/Disney movies well enough ... they're not my favorites.
Had to edit my list for Unbreakable and Dick Tracy.