This is undoubtedly the greatest freeware game of all time.
http://www.miraigamer.net/cavestory/
It's basically a 2D platform shooter/adventure game, kind of like Metroid. It's got really good gameplay, tough boss fights, a fairly good story for the type of game that it is, and even has a secret final level and boss.
Also, Curly Brace is HAWT.