Our favorite is Pecos Bill's. It's a little messy and a little chaotic, but they have really filling burgers, a way cool self-ordering computer station, and a FIX-IN's BAR! Instant Cheese Fries! Many other fun toppings, too. Tons of seating, as well.
If you're lucky, El Pirata y el Perico might also be open (during busy seasons, mostly, but it was open the first week in May 2009). It's basic tacos, but they have their own fixin's bar so you can dress your tacos the way you want. Sort of shares seating with Pecos Bill's, but it's its own counter.
Keep in mind that tourists with fixin' bars make a MESS. If you know that going in, it's less of a shock when you're there trying to dress your own food.