Best Counter Service at Disney/MGM Studios overall (freshness, value, portion size, short lines) is Starring Rolls Bakery (lunch only). They have 2 sandwiches to choose from (panini sandwich w/ turkey, cheese, veggies, and a pesto spread/waldorf chicken salad on a croissant) with chips and a regular drink for $6.99!
If you don't like chips, they will substitute a piece of fresh fruit.
Of all the parks, Disney's Animal Kingdom has the best counter service locations. Of those, My favorite is Tusker House, with Flame Tree coming in at a close second.
At MK, I'm split between different dishes at each location.
Plaza Pavillion's Chicken Garden Salad, with steamed green beans and roasted red potatoes is a real treat.
The Figaro Fries at Pinnochio Village Haus are a tasty snack (although not the most nutritious with cheese, bacon, lettuce, tomato, and ranch dressing on top)
The ham sandwich at Columbia Harbor House is quite good, and unique (broccoli slaw instead of lettuce gives an extra crunch, and sourdough olive bread sweetens the deal).
The taco salad at El Pirata y El Perico is yummy as well, however the location is only seasonal.
Oh! and Caramel Popcorn is back at Sleepy Hollow!!!
At Epcot, try Tangierine Cafe in Morrocco. They have a wide variety, and generous portions.
Best counter service location at Downtown Disney is Wolfgang Puck Express in the Marketplace. They have a much wider variety than their West-Side counterpart (no pun intended).