I don't like to make lists when I go form my most favorite to least favorite because in the end among my favorites it all depends on what I'm in the mood for but my tops ones would be...
In no particular order:
Tim Burton's Batman/Batman Returns - Something as a kid I grew up watching over and over again on VHS, espeically Returns. I actually didn't watch the 89 Batman all the through until about five years ago, yikes! But alas both films have stuck with me. Michael Keaton is my favorite live-action Batman. I loved his suit and the whole style of Gotham. I liked the fact Returns was snowy and featured Catwoman. I like snow.

I thought these two films captured the comics look while maintaining its own style. I even prefer Burton's Batman to Nolan's Batman.
Sam Raimi's Spider-Man Trilogy - Yes, even the 3rd installment. I love Spider-Man, he probably is my favorite superhero. I remember seeing the first film in theaters, I could hardly contain my excitement. With the 90s cartoon, lots of comics to read and action figures to imagine my own stories as a kid I usually always had Spider-Man somewhere in my head. These movies were great at bringing the pages to life with a little hits here and there but not enough to keep from enjoying the films. William Dafoe was a great Norman Osborn and I loved how his influence continued in the 2rd and 3rd films even though he was dead. Alfred Molina was the perfect Doc Ock, from the look to well, everything! With the third film I really enjoyed Sandman and Harry as the New Goblin but didn't care for the Venom stuff too much...the black suit was cool though but I think the whole Venom as a enemy thing could of been saved until a later film. Tobey Maguire was a great Spidey, I only wish we got a couple more films with him and I wished we got to see Dylan Baker's Curt Connors become the Lizard(who is actually my favorite Spidey villain). Even though I was annoyed(more like angry) at a reboot, I do look forward to seeing The Amazing Spider-Man. I just love the character and the universe around him!
Thor - This film pleasantly surprised me. Before The Avengers it was probably my favorite Marvel Studios film to date. I wasn't a huge Thor fan but this film really helped grow into one. The cast was just perfect and Loki has become a villain I always enjoy seeing in comics, animation, or otherwise largely due to this film. I hope we get some Enchantress action in the sequel!
Hellboy/Hellboy II:The Golden Army - Besides Spider-Man, Superman, and The Hulk, Hellboy is one of my favorites as well. And it is largely because of these films that I decided to start reading Hellboy in the first place. GDT had a awesome style to these films that was very reminiscent of the comics. Both films seem to be almost different but yet still the same. Ron Perlman is the perfect Hellboy and I'm dying for one last film with him and Del Toro.
The Avengers - Finally saw this last weekend, the hype was so large that it wasn't until after the movie ended that I fully appreciated it. What a great movie and perfect comic book film. My favorite moments weren't when the characters were fighting but just talking. The dialogue is just fantastic! This showed off how the Avengers is kinda a perfectly balanced team IMO. Plus Iron Man and Thor duking it out is worth the price of admission alone!

Joss Whedon really was the perfect choice.
I would also like to mention the
DC Universe Animated Movies. I haven't seen all of them but so far I have loved everyone I've watched tremendously. Wonder Woman, Batman: Under the Red Hood, and Superman/Batman: Apocalypse are some of my favorite animated films of all time.
I should also mention the
X-Men films, minus the third one which I wish would be ignored. I love X-Men and X2 as well as Wolverine. I have yet to see First Class as I've been waiting on watching it with a certain family member. The Amazing Spider-Man and Uncanny X-Men were the first comics I ever had and quickly become my most favorite so I'm always looking forward to something new with the X-Men and Spider-Man.
I'm sure I left some of my favorites out, but these are in my head right now.