Publick House for Belgian beers especially, though they have a wonderful bottled selection too.
Sunset Grill for a huge selection (both tap and bottle), though not specialized at all.
If you want a really great selection of draught beers from smaller breweries, go to Cambridge Common (in Cambridge) or Redbones BBQ (in Somerville). Don't go to the latter, though, if you want really good BBQ. For that you'd have to go to Arlington or West Newton (Blue Ribbon BBQ).
If you're in Boston only, Charles Street Liquors is great, but if you can go out to Davis Square (on the edge of Somerville and Cambridge), there's Downtown Liquors, which, though a little expensive, is much, much better than even the great Charles Street Liquors in terms of selection.
The Sam Adams tour is pretty good. The Boston brewery is the test lab of the Boston Beer Company; there's no provisions for bottling, the vessels are "small," etc.. It's pretty neat, and the tour / beer is free, though a donation to a local charity is accepted.
And if you're in the Theater District, there's Jakob Wirth, which is largely German-oriented in both food and beer.