Here in the bay: Tony's Pizza Napoletana (chef/owner is Tony Gemignani of World Pizza Champion fame) is probably the best, but we don't really have too many good spots (that I know of). Zero Zero is OK, but their fried chicken/soft serve are probably better than the pizza.
Didn't make it to Pizzeria Mozza down in LA last time. Little Dom's breakfast pizza is the business though.
Edit: If all else fails, Jet keep the engine warm on the runway.