Please share! I have a terrible problem with this, but it takes far longer in third person games than first person. I'm able to play Mario Galaxy for a 2-3 hours before I feel bad, but I'm only able to play Half-Life 2 for five minutes before I have to lie flat on my back for half an hour.
I made more of an effort of unfocusing on the game and focusing on the wall behind my monitor every chance I could get. I also tried moving back to get more 'static' images in my point of view.
I think the problem with Super Mario Galaxy is that now I'm playing it on a fairly large TV that tends to dominate the point of view. It wasn't just me that got sick from it, some friends were over before heading out one night and a few of them tried Galaxy. Three of the four people couldn't get past the part where you are on an asteroid that is fairly small with boulders rolling across it that you avoid without feeling ill.
I haven't had that problem with any other game in a really long time. Not even Portal on that TV (my roommate has it for the 360, I have it on the PC). I would say it was because of the way the camera/screen/world constantly flips and rotates or whatever, but Portal wasn't a problem. We have full 20' diameter dome simulators here, with a 180deg in azimuth and 100deg in elevation field of view (non-motion based) and haven't had any problems in there, either. It bums me out, because Galaxy looked like it was going to be an incredible game.