What to look for:
Try to find a kart that has seen little time. Karts tend to shake themselves to death, so it's important to find a kart that has very few hours or races on it. "Team Karts" are usually a bad idea as they've often seen a hard life, or at worst are cobbled together with parts leftover in the shop at the end of the season.
There are some very good deals to be had on karts that people bought and then got scared of when they took it to the track for the first time. You'll see these advertised as "used only for a few practice days" or "never raced". These are usually a good deal, especially if the person went all out buying all the little extra goodies. Capitalize on their mistakes!
When inspecting a kart, check the frame for any scrapes or cracks, especially at the kingpin or main flex points and welds. Since karts have no [regular] suspension, they have a tendency to crack in important places. If a kart has been recently powder coated, it may have been to hide these cracks.
Try to find a kart with a lot of spares. You don't realize how much a kart stand, bead breaker, spare axle, spare hubs, misc bolts, 3 different jets, kart suit, helmet, etc. etc. all cost until you have to buy them individually. If you can get all of that included in a package deal (assuming all the spares are usable) for a couple extra hundred dollars it will be well worth it.
Links to places to buy from:
T2 RaceKarts (3 time SCCA F125 National Champs)
Fordahl Motorsports (autocrosser from Seattle area)
THE Karting Website (formerly muller.net)
More to come!