Stumpokapow
listen to the mad man
List of PC Humble Bundle games that were not self published
- Penumbra series (Paradox Interactive)
- Hammerfight (Kranx Productions and 1C)
- Bit.trip runner (Aksys Games)
- Shank (Electronic Arts)
- Psychonauts (Majesco)
- Bastion (Warner Bros. Interactive Entertainment)
- Torchlight (Perfect World)
- Vessel (indiepub)
- Trine (nobilis)
- Shadowgrounds (Meridian4)
- Zen Bound 2 (Chillingo Ltd)
- Swords and Soldiers (Ronimo Games)
This isn't definitive because I just scanned Wikipedia for PC versions, often the Linux version was a different publisher. Feel free to correct me if you know that the Humble Bundle funded the developer directly or a game is missing.
Psychonauts is not appropriate for the list--Double Fine bought all the rights back from Majesco, and what was on the HIB went all to Double Fine.
Swords and Soldiers is independent.
I'm reasonably certain the rights for Trine reverted to the dev as well. There was a big kurfuffle, and Trine 2 ended up published by Atlus as a result.
Bit.Trip Runner is independent on PC, although they worked with a publisher on consoles.