I'm sure there are TONS of sequels that I'm forgetting, but here's what I can think of:
Alien3 and Alien Resurrection - the world would be a better place if these films were erased from the franchise (you can throw in the AVP films, too; I haven't seen them but they sound awful!)
Austin Powers in Goldmember - by the third time, all the same jokes weren't funny anymore
Batman Forever and Batman & Robin - the franchise took a huge nosedive once Tim Burton and Michael Keaton left
The Lost World: Jurassic Park and Jurassic Park III - the second one would have been okay if it stayed closer to Crichton's novel (no T-Rex loose in the mainland); the third movie was just pointless
Matrix Reloaded and Matrix Revolutions - I prefer to imagine the first film is a stand-alone because the sequels did nothing for me
Superman Returns - I can't believe Bryan Singer gave up X-Men to make this
X-Men: The Last Stand - I really, really, really wish Bryan Singer made this movie! Brett Ratner was a terrible replacement.
Alien3 and Alien Resurrection - the world would be a better place if these films were erased from the franchise (you can throw in the AVP films, too; I haven't seen them but they sound awful!)
Austin Powers in Goldmember - by the third time, all the same jokes weren't funny anymore
Batman Forever and Batman & Robin - the franchise took a huge nosedive once Tim Burton and Michael Keaton left
The Lost World: Jurassic Park and Jurassic Park III - the second one would have been okay if it stayed closer to Crichton's novel (no T-Rex loose in the mainland); the third movie was just pointless
Matrix Reloaded and Matrix Revolutions - I prefer to imagine the first film is a stand-alone because the sequels did nothing for me
Superman Returns - I can't believe Bryan Singer gave up X-Men to make this
X-Men: The Last Stand - I really, really, really wish Bryan Singer made this movie! Brett Ratner was a terrible replacement.