I'm kind of torn. I like em all, the music and graphics in all of them are fantastic. Cap's is a great throwback, Thor's has a magic of discovery, and IM3's is mega-fun; I've actually watched it on its own more than the others (thanks for the vimeo file, Prologue!). But I think The Avengers and Iron Man compete for the top spot because they feel like such a perfect cap to their respective movies. I'm inclined toward Avengers because it really felt like I had just watched a huge event film, but IM's retro style right after that "I am Iron Man" bomb was so great and original (even with the obvious Sabbath song playing with it).
It's like choosing one of your own childr--
aw **** it, Avengers.
Best as a capper to its film: The Avengers
Best on its own: Iron Man 3 (the graphics and style are simplistic, but they fit really well with Tyler's awesome track)