I'll put in my votes, though I think most have already been mentioned:
Magic Kingdom:
-Columbia Harbor House (if the upstairs is open, sit up there for a relaxing meal away from the crowds)
-Cosmic Rays for the chicken and ribs
Favorite snack location is also found in the MK, a hand-made ice cream cookie sandwich from Sleepy Hollow in Liberty Square.
Epcot:
-Yakitori House in Japan. Nice out of the way place, limited seating but most people overlook it.
-I don't know why, but Electric Umbrella always seems to have the best chicken strips/nuggets on property...
-Sunshine Seasons in The Land has good selections.
Snacks, how can you go wrong with something from the bakery in France? And if I'm on the other side of World Showcase, egg rolls from China's counter service location always hit the spot while waiting for IllumiNations.
Studios:
-Only Counter Service I ever eat in is Backlot Express between Indy and Star Tours.
Starring Rolls has a good selection of snacks.
Animal Kingdom:
-Flame Tree
-Yak & Yeti
-Picnic in the Park in on my list to try, I hope it's running again on my next trip
Downtown Disney:
-Wolfgang Puck Express in either Marketplace or West Side, possibly the best value for your Counter Service credit anywhere in WDW. (My meal was about $19, but easily could have been $22-23)
-I've only eaten at Earl of Sandwich once, my roast beef sandwich was so-so, but people on here rave about it. It's on my list to give a second chance, but haven't had the opportunity.
-Rob