I recently purchased and redeemed the latest humble indie bundle through the USC. All of the games that I've tested so far work great (I've already beaten bastion). I can launch super meat boy, but it only makes my screen turn black and I can hear the game sounds.
I have a nvidia 560 using the latest proprietary drivers and x provided by the x-swat repository. This is on kubuntu 12.04 and my system is entirely up to date. If it also helps to know, I am running a dual screen setup and most games seem to fullscreen to both monitors (as one big desktop).