I was wondering if you guys knew any? Oh, and Dwarf Fortress is too popular. Remember, though, it has to be really innovative.
I'll start it off with three examples.
I'd recommend you check out the FAQ and the Game Design section. Essentially, this game revolutionizes the sandbox genre by making you just another gear in the vast, vast world. Oh, sure, you can stop the invading army, but only if you've fought hundreds of life-risking battles. Until then, Let the army see what it can do (although you can join it). Oh, and if you die, too bad. No saving. Plus, besides, that character was the same as every single other character you have besides skill levels.
When you want to play a game very much just from a YouTube video made from pieces of paper, you know this game is going to be good. Research trees so massive no one person could possibly finish it. That means that you have to rely on other people to help you in this complicated player-based economy. http://www.theuniverse4x.com/story.php
This game revolutionizes the platforming genre. It uses an AI and a random level generator (with a lot of settings) to have a level so complicated... check the Youtube video. If you beat it on the hardest settings, they'll even give you $1000. Oh, and it is possible, as that's what the AI tests out.
Does anyone else know any other relatively unknown games?
Well I usually forget them quite quickly but there is one that came up recently: POP Methodology
Haven't tried it myself but this guy makes it sound very good.
It's a sequel to an older game they made. It has an emphasis on smooth free running and fast, brutal combat. Here's the video that got me interested: