Best Crabcake- I think Galway Bay, odd since it is Irish, but soo good. Also McGarvey's downtown aren't too shabby either, and it's right downtown.
Best Breakfast- Chick and Ruth's is kind of an Annapolis institution although it can be a little crowded with tourists in the summer. They have all your normal breakfast items. The treaty of Paris used to have great brunch, I don't know if they have breakfast. Carrol's Creek is really probably the best restaurant in Annapolis (Eastport it's across the bridge you can also take the water taxi) they have wonderful brunch and dinner, I would try to make it there if you can.
Best Italian is hard I don't consider Annapolis big on Italian, but Maria's downtown in Market square is good. The owner's are Italian... it is especially nice if you can grab one of the outside tables, but that requires some very good luck in timing. I have never been to La Piccola Roma on Main Street, my Mom has she said it was good, but pricey, menu looks pretty good, but if I were you I would skip Italian and go to Carrol's Creek.
Euwwl forgot to mention O'Leary's yes I think Carrol's is second to it, it is really really good for seafood.
I have never really had all that great an experience at Lewnes of course I was always there for lobbyist dinners, but I consider it to be on the same level as Ruth Chris. I am from DC so I rather save my steak night for Rays or The Palms.
Best Crabcake: Grump's Cafe
Best Crab Feast: Harris' Crab House--Kent Narrow's (Across the Bridge) Cantler's if you want to stay "in" Annapolis
Best Brew Pub: Ram's Head if you want strictly-Brew-their-own, otherwise Hero's in West Annapolis rocks-- MANY beers on tap, decent food.
Best Breakfast: Grump's Cafe, again
Best Italian: Don't know, don't eat Italian in this town
With the exception of Ram's Head none of these places are downtown and all are more of a local's hangout.
What you failed to ask, in my opinion is the best place to eat, period, and for my money, it's Galway Bay on Maryland Ave--just down from State House Circle. Irish food to die for!