Empire Strikes Back and Two Towers aside I would have to go with the following:
The Bourne Supremacy - hard, dark, tight and edgy. Total deviation from the book but much leaner and all the better for it. Matt Damon is very convincing and surprisingly sympathetic considering his character's background.
Spiderman 2 - Although I still Kirsten Dunst was hopelesly miscast as MJ (MJ is supposed to be a drop dead gorgeous model) Tobey Maguire rocked the shit out of this and Raimi gave us one of the best comic adaptations so far. Best of all we still have Green Goblin 2, Sandman and Venom to look forward to in Spiderman 3.
If you think of the 3 Clint Eastwood/Sergio Leone Spaghetti Westerns as being a saga then I prefer the Good The Bad and The Ugly to the other two. The three way stand off Eastwood has at the end in the graveyard with Lee Van Cleef and Eli Wallach is a classic.
For Jackie Chan fans, I enjoyed Project A part 2 as much as Project A, even though Samo Hung and Yuen Biao weren't in the sequel. I also thought Police Story 2 and 3 were great follow ups to Police Story.
As a kid I liked Superman 2 as well - he gets to fight other Kryptonians! At the time it looked pretty good.