My random thoughts....
Burgers - Hodad's in OB, Five Guys in Liberty Station, and Classics Malt Shop on Midway...oh also a new place, Jimmy's Famous American Tavern on Harbor Blvd in the Point Loma area makes a mean burger as well - a bit pricey but worth it I think. I also love Tommy's Original World Famous Hamburgers...but I grew up going to the ones in LA...and it's kind of a big thing up there.
Sushi - Harney Sushi in Old Town
Italian - I really like Pomodoro's in Point Loma....try the Spaghetti Carbonara! Also, for a small chain, Pizza Nova is really good...they have a freaking awesome Lobster Bisque and they deliver! I'll give a shout out to Volare (down by MCRD on Barnett) as well....cheap, good - very authentic (I lived in Sicily for a few years...this is the real deal)...but they could use a cleaning crew once in a while though...hehe Solare Ristorante in Liberty Station is good too.
French - Loved Roseville but it shut down...and Thee Bungalow has been replaced by Bo Beau...which is awesome - try the Braised Short Rib Flat Bread...
Greek - I like that little place in the back of Liberty Station off of Harbor across from the Navy Base...by the SS Recruit.
Thai - Antique Thai in the Henry's shopping center on Rosecrans and Midway. Saffron Thai over on India St. is a great place for lunch too.
Chinese - Little Chef in OB is yummy - for take out - too small to eat there really.
High End - Island Prime on Harbor Island or The Marine Room in La Jolla. Can't go wrong with Morton's, Donovan's, Mr. A's, or Ruth's Chris of course. Also recently enjoyed Truluck's in University City...I crave their sweet potato fries now! For atmosphere....try the Red Fox Steak House on El Cajon blvd.
Breakfast - Hash House in Hillcrest or Point Break in Point Loma...they moved into the old Boll Weevil barn-looking building and the ambiance is kind of crusty now but still good food. Perry's near Old Town is great and always packed.
Mai Tai's - Bali Hai on Shelter Island makes the strongest dang Mai Tai you will find anywhere....
Brunch - 94th Aero Squadron in Kearny Mesa or Humphrey's on Shelter Island.
Seafood - I'm not a huge eater of fish, but I do like the shellfish.... I've always enjoyed The Fish Market down on the water near the Gaslamp off of Harbor....and, of course, Point Loma Seafoods can't be beat.
Sandwiches - The Brown Bag Deli on Rosecrans tucked in behind the Angler's Choice fishing shop....(and on the other side is Johnny's barber shop if you want the best haircut you will ever get!)....also, Gus's further down Rosecrans...HUGE subs - get the Philly Cheesesteak...or Pastrami (their pizzas and calzones are good too). If you want a sandwich like your Mom would make, go to Nelly's Deli. Oh, another good deli is at the boat launch over in Mission Bay....not sure what it is called but it is off of Ingraham St. and very good! Con Pane is great as well - they just moved down the street to Liberty Station.
Mexican....Hector's on Rosecrans - he is such a nice guy! Adalberto's on Rosecrans. Buenos Dias Burrito from Santana's for breakfast.... Tin Fish for fish tacos.
Prime Rib - Fiddler's Green on the road onto Shelter Island...they do a nice one.
BBQ - Phil's, of course. Hands down.
Hawaiian - Da Kine in Liberty station is ok for a plate lunch now and then.
British - Shakespeare's pub on India St.
Sunday mornings - the Farmer's Market up in Hillcrest is not only the best Farmer's Market around, but they have some really good food stands! I always like to pick up a Scotch egg or the Sausage and Egg breakfast pastry from Keith the British dude...and a peanut butter hot chocolate from the Joes on the Nose big orange coffee truck...the little woman likes the Aloha Latte...
Wow - I got carried away here! I'm hungry now!