Spiderman 2 for the PS2 is my favorite. They nailed the web-swinging mechanics and the combat was really fun. The only Spiderman game I played that actually made me feel like Spiderman.

The Arkham games are also great, but I found myself bored of them after awhile. And I really don't like how pretty much every recent action game post-Arkham tried to copy the free-flow battle and counter-attack system.