Like 99% of PC games already have native controller support. The only things I would imagine don't support controllers are games like Starcraft, League of Legends, World of Warcraft, etc.
As long as Valve doesn't turn there backs on PC gamers and starts creating steam box exclusives we have nothing to worry about.
Hotline MiamiCivilizationCompany of HeroesFTLChivalryTropicoPaydayTotal War Series (6-12 games)
Most of those just plain wouldn't work with a controller (Hotline Miami supports controllers though). Strategy games are near impossible on a controller. Also, adding controller support is easy as hell on the windows side if you're using Xinput at the very least.
Doesn't matter if it's on XBOX/PS3 cuz THIS IS THE VALVE CONSOLE AND PATENTS AND COPYRIGHTS ARE A THING
Not calling it Gabecube.