While I'm more a Starbucks guy than a Dunkin guy, for diner coffee I like both Soundbites and Deluxe Town Diner.
Soundbites may have a slight edge in quality, but it's self serve, while Deluxe, although not be quite as tasty, is full service and refills pretty reliably.
I like the omelettes, benedicts, and other egg dishes at Soundbites better and both the pancakes and corned beef hash better at Deluxe.
Deluxe Town Diner
627 Mt Auburn St, Watertown, MA 02472
I don't think it's quite what you're looking for, since it's counter service, but on the days when they do brunch (most Sundays) Toscanini's (yes, the ice cream shop) has good food and excellent coffee - Barismo from Arlington, brewed well.
169 Massachusetts Ave, Arlington, MA 02474