Even if you aren't used to liking vegetarian food Sipz Cafe has to be one of the best restaurants in the county period. Amazing Asian fusion stuff, all of it vegetarian and a good percentage vegan. They have 2 locations, one in Clairemont and the other in Poway.
Another vote for Stone. It's well worth the trip to Escondido. The food is excellent and you can partake in some Stone offerings you'll never see anywhere else. Plan ahead and go when you can get a tour of the brewery.
I love Stone's too, but they have gotten pretty pricey and their beer prices have gone up while the serving volume has gone down. Pizza Port in Carlsbad has been one of our favorite haunts when I get to San Diego. All these brewerys have Guest beers. There are great guest beers on everybodies boards.
For a really good and big portions for Breakfast go to 'Family House of Pancakes " in Chula Vista on 'H' St and just 1/2 block south on Broadway,west side of street. It looks like a old 70's style restaurant, kinda small , usually a line or wait on Sat mornings when we go. Believe me its worth the wait, yes the do sell all kinds of pancakes but their omelettes are the biggest Ive ever seen and really good. If you eat a omelette and all the other things that come with it and walk away hungry somethings wrong. I always go for the Chrorizo Omelette and for a pancake restaurant they have better salsa than most mexican restaurants.
If you live in Escondido or at least North County, tHere's a small but very fun place called Jalapeno's on Grand Ave. just west of Center City Parkway. It has outdoor seating with big firepits as well. Mexican food is on the menu but they have American style steaks and prime rib as well. Full bar that pours a cocktail that is worth what you pay for it!