I also hated Beyond the Beyond and SaGa Frontier, tho I'd have a hard time calling them "bad" games, just seriously flawed and definitely not something I'd want to play. Add to this list Shadow Madness, a game whose only redeeming features are decent backgrounds and humor. (And the only really funny character in the game dies in the first ten hours! Unforgivable.)
For true retchedness, tho, check out:
Cardinal Syn - a truly horrible, broken fighting game is painfully bad graphics.
Die Hard Trilogy - I know many people love this ugly ugly game but come on! The game might be playable if I knew what the heck I was looking at, but probably not.
Warriors of Might & Magic - Painful to look at, painful to play. This game has some truly awful controls, dialogue and... well pretty much everything in this game is bad.
Vampire Hunter D - This is a great way to ruin a license right here. Take an interesting character and setting and then drop it into a horrible, uncontrollable mess of a game that has very little to do with the character or setting.