I'm in a similar boat to Kyle in that probably the main set of wheels I wish I could get are a good set of deep dish time trial wheels. Something like a set of Zipp 404's or 808's (though I've never ridden either so I'd have to test them out beforehand to see which works best for me). They'd be specifically time trail/tri wheels.
On the other hand for the mountain bikes: I find the new Crank Brothers Cobalt wheels have to be one of the most amazing looking sets of wheels I have ever seen. From reviews I've read about them they are also an excellent cross country racing wheel. If only! Of course they'd never work with the lefty so they're pretty much out of the picture but still, they are amazing.
For the 29'er I've heard good things about the Mavic CrossMax 29'er wheel set. Not the greatest one out there but a very solid wheel set that would be a big step up from the laserdisc rims laced to no-name hubs that came with the Exile. On the other hand the Velocity Blunt rims laced to your basic deore hub would probably be a pretty affordable and considerable upgrade as well.
I wrote this post quickly this morning just so I'd have it up and wanted to add some things. (There is nothing more fun about day dreaming about bike porn). So, for the 29'er wheels, I like the Edge Composites as built up by Guitar Ted. This build for instance, at just over two grand but weighing in at under 1400 grams, the tubeless version along with DT 240 hubs is tight! Riding a set of 29'er wheels that are over 300 grams lighter then my current road wheels (basic shimano ultegra level rims and hubs) would be a whole new experience. They also look real nice...