I wouldn't want to see games allow cross platform to the point of allowing console players to play against PC players, but only because the difference in control schemes would cause balancing issues. From what I heard about Shadowrun, the devs specifically neutered the Mouse and Keyboard controls by adding some jerkiness to make them less accurate, while at the same time allowing autoaim on the console version -- and they did all that just to make it more balanced.
However, I see no reason not to allow PC gamers to play against Mac and, assuming there is a Linux version, Linux players, and I see absolutely no reason why PS3 players shouldn't be allowed to play against 360 players. Wii players may be on their own, since the hardware is different enough that it generally requires a rebuild of the game from the ground up, rather than a simple port. We already see quite a bit of cross platform play on the PC. There really isn't a way to tell the difference between Mac players and PC players on TF2, at least not since item trading made it so that anybody who wanted it could have a pair of earbuds, and most open source games, like Nexuiz, allow for players on Windows, Mac, and Linux to play together, with no obvious difference on the users end. I guess the real question here is "will the console manufacturers be willing to allow this to happen" more than "is it possible" or "should it happen?"
