The Incredible Hulk is awesome!!! It is very well themed and goes upside down 7 times!! Also, there is some serious speed! It is at Islands of Adventure
I would have to say Batman at SFMM it really has the industrial theme with that entire section of the park. If this thread were best superhero ride, The Amazing Adventures of Spiderman would blow everything away.
I have to agree with The Incredible Hulk at IOA on this one. The theming from what I remember was pretty cool. I don't remember ever waiting that long for it, since the first time i went there was on a day when it was pouring in 2003, and the other trip I had their "fastpass" thing (can't remember what it's called and a bit too lazy to look it up). Even walking through that entrance was nice. It has been awhile since I've been there though, so it is a bit vague for me.
Besides Hulk, I would go with BTR at our park. I love the theming in this ride. I love the car, and the sound effects. The batsuit is great, and I love the huge batman logo on the ceiling of the station.