For a great Mexican (slash Salvadorian(?)) breakfast, I really like Pupuseria La Chicana at West and Main. I've had the machaca plate and the breakfast burrito. Really tasty food- perfectly fried potatoes, awesome beans (I'm positive they are not vegetarian :) ), nice portions. Very reasonable prices and really nice people.
For American fare, I love the pancakes at Savory Cafe, right on main street. They are huge, fluffy and really tasty. Other items are good too, but that's the stand out for me.
Let us know what you think if you end up trying either of them.