What sort of riding will you be doing? Long distance rides on flat roads, climbing mountains, cruising across campus to the nearest liquor store?

For riding around town, get strong wheels and don't pay any attention to what they weigh. Weightweenie-itis is an insidious disease that somehow got loose from the Roadie forum like swine flu.

Deep rims are more aerodynamic but only if you're hauling ass and then only over long distances. And the effect is really only appreciated on rims at 40mm or deeper. They make very sturdy wheels, though, which is why so many ride Velocity Deep-V's.

Light wheels spin up faster so better for quick accelerations. Also better for climbing.

I'd get some Velocity Fusion rims in 32/36 hole and 2x the front and 3x the back. Formula hubs are fine; take care of them and they'll last a long time. Sapim Laser spokes or DT Swiss and you're good to go for a lot less than $400. No disadvantage to using a road hub up front at all.

Use the extra cash for beer.