Batman Begins, with X-2 coming in at a decent second.
Much as I enjoy the Incredibles, I've never been able to quite reconcile it as in the same league as other super-hero movies, much in the same way I wouldn't put Shrek side by side with the Lord of the Rings.
Also, while I enjoy the Spider-Man movies, I find them just a tad too cartoony for my tastes. Same thing with Unbreakable, but in reverse.
Many of the other choices, while good for their time, are sadly dated.