Jagdedge deserves cake for Rez, and so does dylansavage for LBA. Satki gets a nice pie for Warzone, a game I believe was one of the few to get a campaign in an RTS correct.
Okay. My turn. Considering I tend to play games for new concepts no matter how badly flawed they are, I do my best to name games people have never heard of and/or would throw in the nearest landfill rather than play. So the few I'm suggesting are going to confuse some people.
Trust and Betrayal again gets a mention for being the only game I know to actually convince me the computer had feelings and was able to speak in coherent sentances. Carnage Heart, a quirky program-your-own-AI-battling-robot game deserves a remake (and a less vertical learning curve). Blaze and Blade: Eternal Quest deserves an award for beating Final Fantasy Crystal Chronicles to the idea of four player offline multiplayer RPGs by about six years even if it has no economy.
Oh, and Deaththrow for being just a few play balance issues away from being a faithful, fun crossbreed of basketball and Speedball. Chaos League for being the same and a shameless rip off from Blood Bowl.
Topping this list are three strategy games which truly need to be considered underappreciated due to thier amazing content, innovative gameplay, and the fact the game studios STILL were shut down due to commercial failure despite positive reviews. Elixir Studio's two shining glories Republic and Evil Genius are two of the most engrossing experiences I've had in a computer game, and Murkyfoot's Startopia (which could only be described as capitalistic Dungeon Keeper in SPACE) deserves a remake.
Other games that may have made the list if they weren't on the slightly too-popular-but-not-quite-popular-enough side would have been Sid Meiers Pirates! and Uplink.