I'm surprised by some of these answers. I mean, even if you didn't like the game, keep in mind that the question being asked here is what is the worst RPG of all time, not RPG you didn't happen to like very much.
My criteria for "worst RPG" includes whether or not it's even playable. If an RPG is downright boring and terrible but at least it's playable, shouldn't it be better than something that's boring and terrible and unplayable?
Someone did mention the old D&D RPGs for the NES which definitely sprung to my mind. In fact, much of the video game D&D franchise is atrocious. Eye of the Beholder on the GBA, for example, had so many bugs and nonsensical design that it's only fun in discovering exploits.
Aiden Chronicles on the N64 comes to mind. That was painful to play, even for 5 minutes.
Drakkhen for the SNES definitely deserves a mention. I collect games as a hobby and that game holds the distinction in my life of being the only one I have ever returned. If they wouldn't have taken it, I would have tossed it in the trash. It's about as much fun as an apple core or a plastic wrapper so I figure it'd have good company.
Of course, another criteria for worst RPG could be biggest fall from grace: it's one thing when you play a bad RPG, it's another when it's a sequel to a game that you loved and cherished.. If that were the case, a few games spring to mind: Chrono Cross (nothing like Chrono Trigger at all), Legend of Mana (nothing like Seiken Densetsu 2 or 3 at all) and Final Fantasy IX. IMO, worst in the series, and at a time when Square was going out of their way to ramp up their greed: anyone remember PlayOnline?
My friend and I both got FFIX at the same time and suffered through it to the end when we couldn't stop laughing because of the truly awful action/chase scene involving the villain and the main characters. It looked like someone took a background, animated it and then cut out cardboard figures to move back and forth on. For the most part I love the Final Fantasy series but I still can't fathom why anyone would like FFIX (unless it was the first FF game they played and thus had nothing to compare it to).