Humble indie bundle is usually where indie games go to die, sadly
... but I would have to say trine, trine 2 are highly underrated,
beautiful games.
World of Goo. Included in the Humble Indie Bundle #1. Made a huge splash and ended up being ported to the Wii.
Braid. Included in the Humble Indie Bundle #2. For a relatively short indie game, it was well known for a long time.
VVVVVV. Included in the Humble Indie Bundle #3. Received very well by most platformer fans.
Bit.Trip.Runner. Included in the Humble Indie Bundle #4. Like World of Goo, this has also made it to the Wii.
Cave Story+. Included in the Humble Indie Bundle #4. This was on the Wii as well. Do I even need to explain how popular this was?
Binding of Isaac. Included in the Humble Voxatron Debut. Made a big splash and was very well received.
Incidentally, I didn't think Trine was all that good. The controls were somewhat clunky and the puzzles felt repetitive after a while. Different opinions, I suppose.