You might want to call to check, but I believe these places offer gluten-free menus:
Myers + Chang in the South End (fun, casual pan-Asian)
Toro, South End (tapas)
East Coast Grill, Inman Square (seafood, barbecue)
Grill 23, Back Bay (luxury steakhouse)
Casablanca, Harvard Square (eclectic Mediterranean)
Bombay Club, Harvard Square (Indian)
Yoma, Allston (Burmese)
Redbones, Davis Square (barbecue, Southern)
Sabur, Teele Square (Mediterranean, Balkan)
Grasshopper (vegetarian Asian)
Cuchi Cuhi (pan-European small plates)
Fireplace, Washington Square Brookline (New American)
Stephanie's on Newbury (upscale American comfort food)
This suggests that Stephi's on Tremont, South End, their new second location, would also do GF.
Another Chowhound discussion on this topic here: http://chowhound.chow.com/topics/353249
Stone Hearth Pizza in Cambridge (technically a chain, with three locations) now has gluten-free pizza and pasta. While most certainly a chain, Papa Razzi has a gluten-free menu that includes various pastas--not the best thing in the world, no, but it's something.
East Coast Grill has a method that apparently guarantees that your meal is gluten-free. Elephant Walk, as mentioned, is a solid option as well.
I almost forgot: Marco in the North End has gf options, and it's a pretty excellent restaurant. They're quite aware of the whole celiac phenomenon, and bend over backwards to help out. If you call ahead, they'll make GF bread for you, if you can believe it. Move that to the top of the list.
Here's a decent forum that should help you out: