There are so many indie games, but these are some of the best of the best:

Cave Story

La-Mulana

Nifflas's games(Within a Deep Forest, Knytt, Knytt Stories)

Crayon Physics

Also, great idea on the guide. Hopefully it can cut down on the hundreds of "recommend me a game in x genre" threads.

Ninja_Dog

Don't forget Gish!