The Sea Dog in Bangor is supposed to be a good place for microbrewed beers. Not being a beer drinker I can't say from experience, but I've got friends who love the place.
i used to be the bar manager there and always felt that thier beers were more or less a glorified miller lite. not a fan but that is just my personal opinion
#1 Allagash - Allagash White Allagash Black or maybe some of the barrel aged stuff, decisions, decisions
#2 Oak Pond Brewery - Don and his wife are clearly some of the nicest people out there, Nut Brown is wonderful
I'm always pleased when I go home to Maine, as the beer is very good, while being different from our west coast beers.
Some favorites:
Black Bear in Orono
Allagash in Portland
Sebago in Gorham (and Portland)
Seadog in Bangor
Gritty McDuff's in Freeport