Magical Quest was great. There are some good ones so far and for the time being I'll add Way of the Samurai to the mix. That game was so many different kinds of awesome it's tough to describe adequately. It certainly had the best use of a branching story line I've ever seen in a game.

Also, I'll add Resident Evil: Outbreak. troutty online implementation and communication aside, some of those levels were cool, and it had a ton of great ideas; weapon crafting from spare parts, barring doors to slow down zombies, hordes that pursue you relentlessly. I'd love to see a game take those ideas and expand on them, though Project Zomboid kind of does that already I suppose. There aren't nearly enough Zombie games that are about actually surviving the zombie apocalypse.