@Lizzy's Ice Cream in Harvard Square is great homemade ice cream. They have a really good mix of traditional flavors and awesomely unique (and tasty!) ones!
JP Licks is a traditional Boston ice cream store with wide variety of things, from ice cream, to yogurts, to coffee to cakes and pies. JP licks is known for its diverse ice cream flavors. There is one on 352 Newbury St (between Hereford St & Massachusetts Ave).