The game that's probably the worst I own doesn't really count because I knew it would be horrible and just bought it for shits and giggles ("Deadly Strike", some Simple 2000 game brought over by Midas. That just screams "quality"). Great disappointments were Harvest Moon: AWL and Rez, while I have worse games I often expected them to suck.
Hm, while were at it, would be fun to list our collections of crap games and see what gems we can come up with.
Bleach GC (GC) - Or: How to take a series that has tons of things that could make for nice gameplay elements and churn out a completely uninspired game while being surpassed by your handheld division. In one word: Sega.
Deadly Strike (PS2) - Stupid plot, bad gameplay, horrible animations, what more do you want? Disjointed prerendered backgrounds, movesets that give you exactly one useful combo or voice acting in telephone quality? It's all in here.
Lightweight Ninja (PC) - Low quality flashgames with no configurable controls and awful physics retailing for 1€? Sign me up!
Realm of the Dead (PS2) - Because killing Zombies is just so much more fun with unbalanced characters, badly thought out movesets, chuggy framerates whenever anything happens and a camera that won't show anything more than 2 metres away.
The Maid Clothes and Machinegun (PS2) - It's a bad idea to let the player dodge every attack by pressing one button and have no penalty for pressing that button when it's not necessary. It's an even worse idea to put "machinegun" in the title of your game and discourage its use by giving bad grades for using it.
Lufia: The Legend Returns (GBC) - It boasts 200 levels of dungeons. All of which are a 3x3 grid of rooms with small randomness introduced so they could avoid spending money on a level designer. The best way to teach people that "random dungeons" is not a feature but a bug.