Cheers isn't even a "real" restaurant - they sacrificed the restaurant that the TV show was loosely based on in order to create a tourist trap for people who said "OOOH! I want to eat at Cheers!" Skip it.
Legal Sea Foods was great in the 70s (is there anyone here who's really from Boston, and remembers going to the original Legal's in Inman Square - having Bloody Mary's while you waited for your table? Yummm

) and even the 80s before it became overpriced and not worth it - UNLESS you're going there for the fish chowder which has always been, and always will be, spectacular and one of my favorite foods of any kind.
I loved the No Name (seriously, there's no name on the restaurant, that's why it's called the No Name) for years - very informal and great fish; I haven't been there in a while though, and hear that it's gone downhill somewhat. For fish, I'm more a fan of Skipjack's and Atlantic Fish, both in the Back Bay....and if you want an old school feel, the Union Oyster House (near Fanueil Hall/Quincy Market) combines old Boston and really good food.
And Borked is right about the South End - best "collection" of restaurants in the city. To me, the best one to give you a feel of what it's all about is Hamersley's Bistro.
Damn, now I'm homesick, and won't be going back until Spring
PS ADG - Bostonians *hate* it when people call Boston "beantown"
