I was going to look at some of the classic cinemas of Boston's past, but there's really no point of doing so when there's an entire site dedicated to remembering old movie houses. Cinema Treasures is the Wikipedia of movie houses, filled with user-supplied information on movie theaters of the past and present. Included (to date) are 106 entries for Boston. You get everything from nostalgic memories of people who attended openings of The Sound of Music and Cleopatra to detailed histories from dedicated devotees, from architects to name changes and old photos. Even if you know nothing about Boston's cinema past, just browsing the list will provide fascinating stories.
The search page includes a City tab - enter Boston in to the search window and get the full list.