Hi Jennie, for breakfast it would be either the Kona Cafe for sit down or if you prefer a buffet, Boma. I'm a coffee nut so there are few WDW breakfast places that qualify and Kona has the 100% Kona coffee press pot. I usually get the macadamia pancakes or the shrimp omelette (it is not on the menu but if you ask they will make it for you usually)...my wife has been ordering the Samoan lately which is Kona's take on eggs benedict. And sharing a wasabi bloody mary is a great way to start the day.
Boma has a great, nicely diverse breakfast buffet and Joffrey's coffee which is decent.
We usually do just breakfast (2-3x times a trip out and the rest in the DVC room) and dinner - not many lunches. When we do lunch Chefs De France is a nice spot for a break and has probably been our most frequent sit down location.
If we do a counter service our favs in each park are Columbia Harbour House at MK (great tuna sandwich), Flame Tree at AK (Tusker House prior to becoming a buffet was excellent, really miss this), nothing at DHS (used to go to Brown Derby every trip but now the lunch and dinner menu are the same - way too pricey for lunch unless you're just doing the cobb salad) and Tangierine Cafe (Morocco) at Epcot (or if we are drinking lunch as we have been known to do at least once a trip, La Cava Tequila or fish & chips and a couple of drinks at Rose & Crown if we can find a table at the bar).
For dinner, excluding V&A which is the ultimate WDW dining experience, we prefer the signature restaurants with FF, CG and Jiko's our favorites (Citricos and AP close behind). Blue Zoo is quite good also and we are going next month for the first time in a couple of years. We have also popped over the two Emeril's restaurants at Universal (and if you are at Universal during lunch time go to Emeril's for lunch - great three course fixed price lunch for $18-$19).
A couple of late night spots (perfect after Fantasmic or Illuminations) are Raglan Road and Wolfgang Pucks Express if we are going to drive and if not (and we're usually staying around the Epcot resort area), the Blue Zoo lounge for appetizers/drinks, Kimono's for suishi or Big River Grill for a beer/burger.
Another thing we like for late eating is just appetizers and drinks at the bar at FF or CG or a stop at the Crew's Cup at Beach & Yacht or Kona Island Suishi bar.
A key for us is that we always rent a car every trip so we can get around to the hotels and DTD quickly which are the locations that have the places we usually prefer to eat.