1. Spider-Man 3 (2007)
Ah yes. Ever since its release, Spider-Man 3 was a big success at the box office, but critics were mixed, and fans were even more negative (I honestly have a hard time finding someone who actually enjoyed SM3). I, personally, greatly enjoyed the movie, despite its obvious flaws. If they cut back on Sandman (it might have been best to not include him at all...even though Thomas Haden Church was perfect in the role) and added more Venom (heck, if they brought in a much more muscular version [such as in Ultimate Spider-Man) that would've been great), and shortened the length some, then it likely would've been more on par with its predecessors. I rate Spider-Man 3 a 4.5/5.
2. Batman Forever (1995)
As a sort of preface, I wanted to note that I have not seen Batman & Robin (and I have no intention to do so), so I can't give a complete opinion on the original Batman series as a whole. The biggest weaknesses in Forever were the much more family friendly feel (in exchange of the darker mood with Burton's movies) that ultimately resulted in very cartoony Riddler and Two-Face, and the swapping of Michael Keaton to Val Kilmer in the role of the Caped Crusader. Personally, I think Kilmer has more of that Bruce Wayne look than Keaton, but it's hard to consider Forever as a sequel to Burton's two go-around's because the change of cast doesn't make it connect well enough with the first two. So overall, I consider Batman Forever to be the weakest comic book movie I've ever seen, with a rating of 2.5/5.
3. Pirates Of The Caribbean: At World's End (2007)
I became a fan of the franchise a month ago when I saw Black Pearl and Dead Man's Chest. AWE still contains those thrilling action scenes, but the plotline(s) made it very confusing to follow, and overall a disappointment compared to its predecessors. Also, it was way too long in length. Still, I found it to be a mostly thrilling adventure that concluded the trilogy, and I give it a 3.5/5.
4. Ice Age: Dawn Of The Dinosaurs (2009)
The Ice Age franchise has always been one of my favorite animated movie series, and I personally found the third entry to be the best yet. Sure, the plotline is kind of unoriginal, but the animation is fantastically bright. I give Dawn Of The Dinosaurs a rating of 4.5/5 (if not the big 5).
5. Shrek The Third (2007)
I've never been a fan of the Shrek franchise (the first two are still some of my least favorite movies of all time). The third one was a surprising step up (or at least in my opinion). Most of the flaws that were with the first two (such as the unneeded crude humor) that weakened the first two are still present, however. I rate Shrek The Third a 3/5.
6. Star Wars: Return Of The Jedi
Yes, I'm definitely one of the bigger SW fanatics out there to say the least, and I thought ROTJ was the best of the original trilogy. Sure the first was really good, and Empire Strikes Back was pretty good, but ROTJ had more to like (in my opinion, of course). Unfortunately, it's commonly considered the weakest of the original trilogy. Given it's one of my favorite science fiction movies of all time, I rate ROTJ (also known as Star Wars VI, given the prequels) a 5/5, without a doubt.
And I know there are many, many threequels out there. But these are a few that weren't appreciated as much as the originals or twoquels of different franchises. And another thing...some threequels that were commonly poo-poo talked (such as X-Men 3, Superman 3, etc) I have yet to see, so I can't include them here.