Haven't been in about 20 years, but Toscas in San Diego was just amazing. Like most things, has probably gone downhill.
I still love Zachary's in Berkeley, and this little bohemian hole in the wall in the SF Fillmore District that I can't quite remember.
But, as several have noted, NYC pizza is amazing, just about anywhere you get it.
A couple in Indy I love, Bazbeaux, and Eh Formagio!