People, stop taking these lists personally. No need for ridicule just because someone likes a game you don't like, and vice versa.
Oh don't be such a pussy.
Anyway, I have only played about half the PCE library, and I've probably played most of the great games, and missed a lot of the bad ones so I'm not very knowledgeable about the really shitty stuff. Basically these are games that really disappointed me, although I'm sure there is worse stuff:
Renny Blaster: This thing sucks. Sure is a better game than, say, Energy, but I hate it far more.
Neketsu Soccer: This sucks because its basically the FC version with 1% better graphics and some really shitty cinemas thrown in. I love Neketsu games, but this one was just an excuse to reprint the game.
Cal II: Terrible.
Cal III: The terrible sequel.
Tony Hawk's Riot Zone: A mediocre rip off of the mediocre Final Fight. Boring a tedious as hell.
Martial Champions: I hated the arcade game, and this version is even worse. I'm a huge fan of 2nd tier fighting games (Vampire, Waku Waku 7, Real Bout), but this thing isn't even close to 2nd tier.
Graduation: I f*cking hate this perverted shit. I mean, something like Prostitute Maker (DOS) is far less offensive to me since its honest, outright nastiness. Graduation is totally G rated on the surface, but truly ota were spanking themselves to this thing 24/7, and it makes my stomach turn.
...that's all I can think of.