I second the tip top meats req. Fidel's on the coast off Carlsbad village drive is kind of a classic as well, though I'm not blown away by the food. Pizza Port off carlsbad village drive is good, Azafran for Cuban in Oceanside, Mozy's in Leucadia off the 101 for healthy delicious burritos, La Especial Norte off the 101 in Leucadia for insane soup.. St Germain in south Encinitas off the 101 has the best bacon I've ever had, great for breakfast/lunch.
If you are a fan of traditional sushi, or are curious to see what it's like, there's no better example of traditional sushi in San Diego than Kaito Sushi in Encinitas. Check out their reviews on Chowhound or on Yelp for the buzz and more info.
Also Yumeya in Leucadia (northern Encinitas) is a cozy family-run Izakaya (Japanese pub) with a huge sake selection and small bites to compose your meal. Reservations highly recommended.
A nice place to pick up a dessert (not eat in) is Elizabethan Desserts in Encinitas. Desserts in an American Nostalgic style with upgraded ingredients and technique.
Bety's Tacos is not your typical "SoCal Mexican" fare, but a small individually operated sit-down eatery (order at the counter then choose your seat) using traditional family recipes. A good place to discover something slightly different than what's usually offered-up as Mexican food in the 'burbs of SoCal.
A great place for breakfast 2 towns south in Solana Beach is the Beach Grass Cafe. They have a second location in Encinitas that I haven't been to, but even on looks alone I'd drive the extra distance to Solana Beach.
For an incredible Carne Asada (order the plate or Torta to get the Arranchera cut) go to Rudy's in the Eden Gardens section of Solana Beach. They have a second newer location in La Costa, but my vote still goes for the original one in SB, co-located inside their Mexican market.
Located inland from Carlsbad is Pho San Marcos in, well, San Marcos. It's an incredibly tasty Pho, actually my favorite in all of San Diego, in an area and city that "shouldn't have" any good Pho!
130-A N El Camino Real, Encinitas, CA 92024
1246 N Coast Highway 101, Encinitas, CA 92024
155 Quail Gardens Dr, Encinitas, CA
Betty's Tacos Restaurant
1464 Encinitas Blvd, Encinitas, CA 92024
159 S Highway 101, Solana Beach, CA 92075
Rudy's Taco Shop
524 Stevens Ave, Solana Beach, CA 92075
Pho San Marcos
700 S Rancho Santa Fe Rd, San Marcos, CA 92078