I haven't been everywhere, but my top three places are:
Best Overall: All-Star Sandwich Bar in Inman Square. The sandwiches are fantastic, the side dishes are tasty and affordable, and the new ownership is friendly and ambitious.
Best Deal: Harvest Co-Op Deli Counter in Central Square. It depends to some extent on who waits on you, but I don't know of another place where you can get a quality, good-sized sandwich for $5 ($6 for meats).
Cheap and Best: New Saigon Sandwich in Chinatown. Tasty but airy sandwiches for $3. Add an exotic shake for another $2.50.
Am I missing out on anything better?