We usually do a combination of sit-downs and counter service, but the sit-downs we choose at WDW are more for atmosphere than for food; places like Sci Fi, 'Ohana, Rainforest Cafe, character meals, etc. The rest of our meals are counter service.
Some of our favorite counter service experiences:
MK: Peco Bill's - Great burgers and fixings bar. Columbia Harbour House - DH enjoyed the fish and chicken, and I loved the veggie chili. We liked this one so much for lunch, we went back for dinner the next day! Casey's - Great hot dogs, and I don't even usually eat hot dogs!
AK: Pizzafari - Good pizza and salads.
Epcot: We've had several great counter service meals here, including Yorkshire County Fish Shop in England, Cantina de San Angel in Mexico (great wet burritos), Boulangerie Patisserie in France (Yummy!) and Sunshine Season Food Fair in The Land.
MGM: No counter service here, because Sci Fi is a must-do for us!