Breakfast in Benecia
Either the Shoreline or First Street Cafe are your best bets, both located on ... you guessed it, First Street.
The Shoreline has a somewhat sterile room, but nice views out to the Carquinez Strait and the new Carquinez Bridge. Good traditional breakfast fare -- omelettes, french toast, etc., along with a few twists. There corned beef hash scramble is actually pretty good.
First Street Cafe is a nicer space, looking out on First Street. Kind of a funky 70s throwback space, with good coffee and breads, and good solid traditional, if not particularly inspired, breakfast fare. There fruit crisps and other desserts, on the other hand, are very good, but they work better in the evening, particularly if you head there on one of the nights they have some acoustic musician playing upstairs.
Benicia from a native! (note the correct spelling)-
I second First Street Cafe for breakfast. Good portions, tasty food, nice environs. They prepare as fresh as you're going to get for the town. If you are a scone fiend, try their scone of the day.
Take a stroll on First Street afterwards as there are neat antique and other stores.