I was thinking some more about this, and there are really sort of two different categories here... sandwich shops - which have had a pretty significant market presence for a long time, and "everybody else". In the latter category, there are the "near-fast" mexican places, pei wei, wow bao (popular in Chicago), La Madeleine, etc.
Another sandwich place I love is Potbelly; yummy sandwiches there. Jersey Mikes is in that category, but I do not care as much for them. Used to love Blimpie, but they seem to be getting run out of business by subway. I count Scholtski's Deli in this category as well; though they always struck me as a wanna-be Quiznos.
Then there are the delis: love Murphys Deli mufalettas, Jason's Deli, and McAllister's Deli. For my money, Carneghie Deli in NYC is the best - their hot pastrami on rye is to-die-for.
Panera Bread (free wifi ^ ^), Au Bon Pain, and Atlanta Bread Company are sort of cross-overs somewhere between sandwich shop and deli.