Currently Valve does this, and there are mechanics from within Steam to facilitate this. Games can have "Steam Play", which means if you can install Steam on that machine - you should (in theory) be able to play the game on that machine.
Any game you buy that has "Steam Play" enabled lets you download whatever version appropriate for your system. For example, Portal 2 is (or has been) releasing for Linux recently, and if you've bought the Windows version, you do not need to now go and buy the Linux version, you just click to install it while on your Linux box.
I'm really hoping developers will use this - even for their years-old games, because the point brought up a few replies back by DoofusOfDeath is true. I really hope some of the first newcomers to the Linux marketplace won't be turned off because a port of their 7 year old game didn't sell as well as their Windows counter-part did.