I'm only considering the ones that were big letdowns. A lot of sequels weren't quite as good as the original, but they were still very worthy sequels and didn't disappoint, so I won't name those.
Movies:
Cube 2 (see below for my take on it).
Indiana Jones and the Temple of Doom wasn't one of my favorites simply because it deviated really far from Raiders of the Lost Ark (thankfully, they returned to the Raiders-style action in Last Crusade). I haven't seen Crystal Skull yet, and probably won't because I liked the series ending on a high note in Last Crusade and don't want it potentially ruined.
Matrix: Reloaded and Revolutions. Is it just me, or did the storyline take a turn for the nonsensical? Half the time I don't know what the hell is going on. At least Reloaded had some pretty good action scenes though, but for me the highlight of the original was the story. Revolutions...well, it just felt like a chore to watch. The idea of Neo being fueled by love or whatever (forgot which movie that was introduced in) made me want to projectile vomit across the room at my screen.
Games:
Mario 2 doesn't really count because we all know what the real version of SMB2 is.
Frogger 2: Swampy's Revenge. This is a fairly obscure one. For those who don't know, Hasbro released Frogger: He's Back!, a 3D adaptation of Frogger, where he has new abilities and more importantly new worlds to explore. The gameplay was great, the worlds were excellent, and the soundtrack kicked ass. Then came Frogger 2, with annoying controls, lack of creativity, only a few interesting levels, and an inferior soundtrack, resulting in an overall disappointing sequel.
RC Revenge: Even more oscure than the one above. Its predecessor, Re-Volt, was an RC racing game that plays a lot like Mario Kart, with items and such. It was simply a fun game to play, and it actually had realistic physics, unlike a lot of racing games. The physics made the game a lot more challenging because you actually had to be a good driver to win. You could also build your own tracks and race on them with a pretty flexible track editor. Then came RC Revenge, which took everything good about Re-Volt and discarded it. The realistic physics are gone, and in its place are very clunky unresponsive physics. The tracks were fairly dumb, the track editor was very limited, and to top it all off, it had both vastly inferior graphics AND framerate. There's simply no excuse for that, being that it's a sequel and not a prequel.
Final Fantasy IX: Though not a sequel in a technical sense, I think this deserves a mention. This was the one that turned me off from the series. Zidane...let's just say I don't like this guy. The main bad guy isn't any better, and combine that with a lame love story and one of the most random endings ever (complete with a final boss out of nowhere), I could see exactly what road this series was going down.
Did you see the same movie as me? Because when I watched Cube 2, I saw a badly written, badly thought out, badly executed ball of crap with some horrendous acting to boot. Everything about it was pure suck.
*begin big Cube 2 rant, complete with spoilers*
I completely agree with you. Being a huge fan of the original, when I saw Cube 2, I was shaking my head in disbelief, saying to myself "How could they have fucked it up this badly?" The first big problem I have with it is none of the characters are likeable, they're all extremely irritating and I found myself rooting for the traps instead of them. The only one who was remotely half-tolerable was the guy who kept getting eaten near the end, but even he was annoying with his peppy attitude. Half of the characters were complete throwaways with no character development at all (see below).
Another thing that got on my nerves was the random interjection of a very weird, completely pointless love scene between the two most useless characters. When you're narrowly dodging death traps in every other room of a 4D tesseract, there are no love scenes. Period. The group even had the exact same structure as it did in the first Cube. Just replace Quentin with that jackass who kept collecting the watches, and there you go.
To top it all off, the biggest complaint I have is that the logical problem-solving steps that were present in the first movie are gone. In Cube, the characters used their collective minds to figure out just what the hell is going on, how the cube is constructed, and using this knowledge, they construct an escape plan. In Cube 2, they come across a dead mathematical genius who wrote all over himself, promptly decided "This problem is impossible, let's spend the rest of the movie wandering aimlessly with our thumbs up our asses and only a vague clue as to what's going on", and right near the end they discover "This cube is imploding, nevermind why! Let's get the hell out via (quite literally) a plothole!" And to top it all off, the only surviving character is executed, as if to say "fuck you for watching this movie".
Thankfully, Cube Zero was somewhat better, and they did away with all the super high-tech bullshit (returning to the original dark, gritty atmosphere), but it still wasn't as good as the original in my opinion.
*end big Cube 2 rant*
Man, that was a long post. Sorry about that.