When I was an undergrad at Berkeley, one of my favorite pizza places was Zachary's Pizza in Oakland, by the Rockridge BART station. Zach's was always crowded and always good. I think that was one of the first times I'd actually had pizza as a real pizza "pie". Many years out of undergrad later and not getting up to Berkeley or Oakland hardly ever, I was delighted to discover Patxi's (pronounced "pah-cheese") Pizza in Palo Alto thanks to my friend Karen (http://www.patxispizza.com/).
Patxi's is the closest I've come to Zachary's pizza on the peninsula. Their deep-dish Chicago-style pizza has a buttery crust and is laden with cheese. Yeah, don't go there if you're dieting or counting calories. The pies take anywhere from 30-40 minutes to bake so I've discovered the best thing to do is call ahead about 45 minutes before you expect to arrive (and account for having to hunt for parking around Palo Alto's busy University Ave) and order for dine-in. Then it's just a matter of arriving on time and they serve your pizza within a few minutes. If anyone in your party is late, they can also hold the pizza for you in their warmer. The call ahead option is a boon, especially when you're meeting cousins with young kids who probably wouldn't appreciate waiting more than half an hour for pizza :).
Oh, and once again if you're not on a diet and not watching what you eat (although you, I mean, "I", should) and have partners in crime who also like a little dessert, there is also conveniently a gelato place located next door to Patxi's so, despite being full, if you wanted a little something for your sweet tooth, you could also stop there on your way out to your car. I can personally recommend the mocha almond fudge. Just sayin'.....