I treat them like real life colleges. Some are prestigious (Redhurst Academy of Magic is the Harvard of my world, with all the connotations), some are good but unexceptional (St. Feldin's College of Abjuration in Tarsis) and some are simply adjuncts to other colleges (the wizard school at Rashadar College in Uraq).
Dragon had a nice article a few months ago ("a few months" means up to two years in my brain, not sure when it was, exactly) with new wizard colleges that were pretty clever.
Still, the Cadillac of wizard colleges is the Redhurst Academy of Magic. You can get the Player's Guide free on the Human Head Web site, which includes everything that's not reserved for DM use. I believe the entrance requirements are in the guide.
For other schools, I use the guidelines given in Complete Arcane for the Arcane Order: Tuition is 750 gold for a one-time entrance fee, followed by 30 gold/month for a year-round schedule. Redhurst is a lot more than that, but comes with many more benefits.