Here are my suggestions:
Centre Street Cafe - there is always a very long line on Sunday mornings for brunch but it is absolutely worth it. Fresh, surprising (but not weird) dishes that are as big as your head. Come hungry!
Bon Savor - small place on the corner of Centre and Pond street with a basic array of french toast, pancakes, and omelets.
Cafe D - One of JP's favorite bistros - a little more high end than the average JP local but cool atmosphere and tasty food.
Doyle's - old style Irish pub. I can't vouch for their brunch but they do have it. Bangers and mash anyone?