I second the Motorino rec, went there a couple weeks ago right before I flew back to school (': Also get a slice of artichoke pizza at Artichoke Basille's Pizza.
And then the rest of my recommendations are dessert... One of my favorite things ever is cereal milk soft serve with crunch from Momofuku Milk Bar, and the crack pie from there is also awesome. Big Gay Ice Cream is amazing as well. Veniero's has a huge selection of Italian desserts and pastries, which are all fantastic. Spot Dessert Bar is also one of my favorites.