I'm not sure I could make a definitive list either. I do think that, for the most part, that first Avengers picture is really well put together. Otherwise, I have a fondness for the first Thor film, I find that Branagh was a very fitting choice to implement the pseudo-shakespearian aspects of those early Thor comics. Similarly, the first part of The First Avenger is a really great watch. Feels just like Johnston's adaptation of The Rocketeer from ten years earlier, which I maintain is an excellent movie – in some ways perfect.
I find that I have more of a fondness for the early Marvel movies of the early 2000s, as they were the movies of my youth. The first Spider-Man has always had a special place in my heart (especially since I have developed an affinity for Evil Dead II) and Ang Lee's Hulk has become a favorite of mine as well. I think his background in family centered dramas in Taiwan positioned him well to tackle the psychological aspects of Hulk which have made him one of my favorite characters. Even that editing gimmick I find really fun!
A different response than you were probably anticipating, Luke, but I can't help myself when talking about movies