Spider-Man 2 is still the best one, IMO. I loved the power loss/Spider-Man no more story. The way the burden of being Spider-Man was weighing heavily on Peter's life and having disastrous effects. He couldn't hold down a job. He was failing at college. He was getting alienated from MJ, his friendship with Harry was suffering. All of this made for great drama and I think it mad Tobey Maguire give his best performance of the trilogy.
I think the supporting cast in Spider-Man 2 were used really effectively, too. Aunt May, Jonah Jameson, MJ, Harry, they all had meaty roles in the story, and none of them were just there for the hell of it. But my favorite part of Spider-Man 2 is the villain of the piece, Doc Ock, played with great skill by Alfred Molina.
Granted Doc Ock was changed in certain aspects of his character, but he was nonetheless a compelling villain IMO. Some of my fav scenes with him include:
-The demonstration scene. When he strapped on the tentacles and willed them to life I got goose bumps. Loved the bit where he viciously swiped Spider-Man away when he tried to unplug the reactor. A little foreshadowing of the violence Octavius was capable of to make his dream succeed.
-The scene in his warehouse lair where he turns evil. The creepy music, the way the tentacles wavered around his head menacingly, how he slowly comes around to their influence with that lunatic smile "Yessssssssss"
-The cafe scene. He was really menacing in this scene:
Ock: "I want you to find your friend Spider-Man. Tell him to meet me at the West side tower at 3 O'Clock"
Peter: "But I don't know where he is"
Ock: *Removes his shades with a tentacle* "Find him. Or I'll peel the flesh off her bones"
Peter: "If you lay one finger on her...."
Ock: "You'll do what???"
-The scene where the train passengers stood up to him to protect Spidey, and he just grinned and swiped them all aside.
-All the fight scenes with him rocked. Every single one.
Spider-Man 2 is the jewel in Spidey's crown as far as the movies go.