Yes, they're over-priced at times... yes, the stores can be crowded.... but the service is always excellent, and the quality is always top-notch.
I work across the street from the Yorkville store, and it is the only place I will go for a coffee (they have a good selection of teas as well) and a pastry. I think that's saying a lot, because Yorkville has a lot more options than just the obligatory Tim Horton's and Starbucks.
The lunch counter is well-stocked with choices (tons of salads to go with all of those sandwiches, pastas, etc), and the staff are efficient, friendly, polite, and knowledgable. Also, since I don't buy my lunch every day (I'm a brown-bagger with swagger!!) I don't mind paying more for good take-out food.
Also, for such a small store, they stock a LOT of different cheeses. Everyone gets extra points for having lots of cheese:)