These games from the Humble Indy Bundle have not been released under a free license, nor does it appear they will be. All that is being released are their engines.
Following the ID tradition.
There are already dozens of free software game engines available with no free software games which use them.
And because of Engine only releases Open Source developers have been able to produce a host of new games. From the Quake engines alone we have Tremulous, Warsow, Alien Arena just to name a few.
Having a proven Engine under your Project allows developers to focus on Assets and Level Design and tweaking the gameplay to a much larger degree than is possible if developing the engine as well.
There is another benefit to the original developers and users in that their games survive onto the next era of computing and gaming devices.(iPhones, Androids and insert your favorite tablet device here)
I bet the human brain is a kludge. -- Marvin Minsky