There's no overall "best eatery" in town. Any specfic things you are looking for? If you want to mash crabs, all the D.C. weekenders always go to Cantler's, which is run by a fine family, but we all (natives) go to Mike's (on the South River). Neither of those are right in town. Downtown has plenty of excellent seafood (but Annapolis is NOT a cheap food town): Carrol's Creek's crabcake (ugh, try saying that fast), O'Leary's if it is still around, Sam's. Do not got to Buddy's or Philip's, just tourist mad scenes.
Otherwise, it's tough to say--there is definitely a potentially unhealthy symbiosis between the local restaurants and the nostalgia/ unearned loyalties of locals. I always have to go to Riordans for a burger when I am back there, friends have to get clams at McGarvey's, and we go to Middleton's because we always have (all at the City Dock)--and while I think these are all really good, I'll be the first to confess that sentimentality may be hard at work here.
Oh, and cheesesteaks at Chris' Charcoal Pit on West Street (not in walking distance from town) and donuts from Carlson's bakery, also on West Street a little closer to town, were always excellent, but I haven't made a trip back to either in years.
Hope this helps. By the way, unsnapping the "Caps Lock" key makes posts much easier to read.