Star Wars Episode 1: The Phantom Menace - Yeah this was never going to live up to the hype, no movie could ever live with that sort of weight of history on its shoulders. I actually prefer this to the other prequals, the final lightsaber fight, pod-race were decent at least but yeah always going to be dissapointing.
The Lost World: Jurassic Park - Never cared much for these films, dinos in movies dont really do it for me.
The Godfather Part 3 - Didn't get a chance to see it.
Spider-Man 3 - Should have been so so much better after all the hard work done in the first two, a massive dissapointment which clearly had troubles due to studio tampering.
X-Men: The Last Stand - Much like S3 it had a troubled life, Singer leaving the directors chair started alarm bells straight away and then casting people like Vinnie Jones only rammed home the conclusion this would be a mess which it eventually was. Again should have been so much better.
Tron: Legacy - Anything had to be better than the laughably bad original film. Legacy wasnt great other than in the looks department but looked like an improvement to me. Guess I'm not the best to judge on this one.
Indiana Jones and the Kingdom of the Crystal Skull- Looked and felt like a cash grab, they never had a decent story in the first place it seems.
Godzilla (1998) - Was never into Godzilla so never expected much from it anyway and was pretty dull.
Its a toss up between S3 and X3 I guess for me both had the chance to close out a great trilogy but instead they fumbled with the endzone in sight. I think I shall go with X3 just because someone thought this was a good idea:
PS: Can I give an honorable mention to The Matrix Revolutions for being a total let down as well and should be on the list.