The Courtyard Cafe: Located on Quincy street in the downtown area, the Courtyard offers a $3.99 lunch special of homemade soup with homemade bread. Both are yummy and the meal is filling for a singe person.
Subway - Located right across from the ferry landing, this Subway is no different than any other, but the $5 sub is a good value and is customized to your order. They have a regular menu of $5 footlongs as well as a footlong of the month.
The Little Rose - This one deserves it's own blog entry, which it has, so go check it out too. if you bring your own container, you get to pick 3 entrees plus rice from 10-12 dishes for only $5. Tasty and abundant enough to share. They're located on Adams St in the downtown district.