It has become apparent over the last few years that one of the more reliable destinations for the more adventurous theatregoer is the Charlestown Working Theatre.
Molasses Tank Theatre is currently receiving great praise for their Conquest of the South Pole. (which I won't be able to see, but desperately want to.) They take their name from the unfortunate disaster in Charlestown which fascinated me when I read about it in an SRA kit in elementary school.
Take a look at their production history here. They really program some interesting work.
Theatre On Fire, turned some heads at the same venue with their recent production of Race.
And Whistler in the Dark Theatre Company has presented the works of such playwrights as Howard Barker and Eric Overymyer there, although they have spread out recently to other venues. Whistler will be presenting Will Eno's The Flu Season at the Black Box at the Arsenal Center for the Arts, which, coincidentally, is where Eno's Thom Pain, had its Boston premiere by New Rep last fall.