I'm trying to figure out what wheelset to buy and I can't decide between tri-spokes or deep rims (like Zipp 404's). Any ideas?

Well get specific on what sort of racing you are doing, what speeds you average currently, your aspirations etc. Do you do road racing as well? (the Zipps could come in handy for road racing as well)

Brendon

if you're doing only tri's, go with the tri spoke/dish wheels, but if you wanna race road, or ride a lot of road, especially with groups, then go with deep rim aero wheels

Buy your wheels based on the type of racing you'll do. Consider what type of racing, and especially the courses. Companies make wheels that are better for windy conditions, hilly courses, etc. Do some research to find out these details and then decide what you want to do with the wheels. For example, you might not want tri-spokes for a super windy course (if it's known for heavy crosswinds) or a super hilly course when the zipp 404's would be a better option for the hills and really might not make a noticable difference overall. IMHO, I'd look for the most versatile and lightweight wheel, and then focus on training myself to produce the power needed - not the other way around, which I see a lot - where people focus on buying these crazy expensive wheels in the hopes of dropping significant amounts of time from their bike split when it really isn't the wheels that much unless you're talking about the elite competitors (where their cycling abilities are so close that the wheels actually can make the difference in seconds between bike splits).
The Zipp 404s are a great set of wheels though! I'd go with those. Check out the Reynolds as well. They make some nice deep dish rims.