I am going to be in San Diego for two days at the end of September. Would like to visit La Jolla also. I know it's a very short time to squeeze those two places, but that's what I have - two days. What are the must-see in SD and LJ. I'll have a car.

TahitiTams can probably priorize better than I but we like in no real order.
Balboa Park
Coronado Island
Oldtown
Pacific Beach
In La Jolla
the village
La Jolla Cove
Childrens Beach ( sea lions )

I think hulajake has a good list, but i would nix Pacific Beach especially if you are spending beach days in Coronado or La Jolla.
You could hang out in La Jolla on one day and go to the Cove, Children's Beach to view the sea lions, and walk around village.
The second day you probably could do two things (for example Balboa Park and Coronado) but Balboa Park, Old Town and Coronado in one day might be a bit too much.
Restaurants in La Jolla - Pannikin for coffee, El Pescado for lunch, dinner Zenbu - sushi, The Cottage, George's (upper level), Piatti's in the LJ Shores area.
The Shores is also a fun area for beachbumming around. There are many surf shops, canoeing rentals etc.

Coronado has some good restaurants too: Tent City, Miguel's Mexican Cantina, Il Fornio, Brigantine.

I think that is doable in 2 days. It will be be busy but it can be done. Start out early. It would help to know where you are staying? Also not sure what the village is? Seaport Village perhaps? That is just shops. One could eliminate that place. Old Town isn't what it use to be. Pacific Beach is just a drive through along the beach. Nothing really special there. La Jolla and the cove, and maybe lunch or an early breakfast in La Jolla would be wonderful.

i think the village is La Jolla Village...

Hi kiramoli..
Everyone here has given you excellent advice and the end of September will be gorgeous.
Have a great time in SD!

Aloha hulajake!

I like Pacific Beach a lot and definitely wouldn't skip it, but your choice will depend on what you are looking for. Both La Jolla and Coronado are more upscale whereas Pacific Beach has more of a typical California beach town atmosphere with people riding around on cruisers, mix of funky shops, surfing, and so forth. Pacific Beach is more of a party than Coronado or La Jolla.

If you get a chance, visit the Scripps Aquarium in La Jolla. It's small, but a wonderful place. The highlight: when you go out in the back to the Aquarium's tidepool exhibits, you have the most incredible views of the ocean and surfers.
I would also visit Old Town.

Speaking of views if time permits try a ride up to Fort Rosecrans where the light house is located. If it is clear, you will also see some incredible views. On a "clear Day" you can see forever. It is a must see. There is also a little harbor cruise down by the embarkadaro if they still run it. It takes you around the harbor you see ships, and it is about 45 minutes long. Nothing earth shattering, but touristy, quite often you will see Seals lounging around on piers.

Thanks to everyone who posted. I'll be staying at Westin Horton Plaza, my husband has a conference to attend.
The itinerary that I came up with the help of Fodorites:
Day1 - morning - visit La Jolla: village, Cove, Children's Beach. Have lunch at George's on the terrace.
Do I need reservation? I'll be there on Saturday.
Afternoon- back to SD. Old town, and may be Gaslamp district. Is there an Old Town Trolley?
Dinner at Old town or Gaslamp.
Day2 - Balboa Park, San Diego Zoo. May be Coronado in the early evening.

Does it seem feasable?
Any recomendations for a good seafood restaurants in Gaslamp/Old Town and Coronado.

You don't need a reservation for George's Terrace. They only take reservations for 50% of the tables. However, I would advise making one if you want to avoid a potentially long wait as it's always busy.

the last day is a bit too packed. i would Balboa Park and Coronado, unless you have never been to a zoo before. I also prefer Wild Animal Park to the zoo as it's more unique. A zoo is a zoo, similar to other zoos.

I would also make sure to make it to Gaslamp one night. It's most interesting in the evening, especially if it's a weekend. Make your dinner reservation for dinner there unless you really want Mexican food in Old Town instead. There could be a long line for the best restaurant in Old Town too on a weekend night.

George's is spectacular but if the breeze is coming in off the Pelican Rocks...well, it can affect the ambience. Instead, come lunchtime, drive 10 minutes down Mission Blvd to Mission Beach, to a wonderful place called The Mission. You will have a fabulous meal, in a wonderful atmosphere, for a great price. They only serve breakfast and lunch. You'll be surrounded by locals, too--no tourists And it's a better choice if you have a child with you. George's is expensive!

George's Terrace isn't expensive. Wear a light jacket.

I agree with Barbara that George's isn't expensive on the terrace and in SD, you always bring a light jacket..

The Mission in MB has locals and tourists and the food is good but I don't see it as a must..imo

Your trip is too short for this but if I were coming (I live here), I would do a kayak tour in La Jolla shores...it is spectacular. We saw leopard sharks swimming beneath us and garibaldi and were 10 feet from sea lions in the water.

Can I ask which Kayak Tour you did in La Jolla? Will be there next weekend.

George's is a very expensive, and probably inappropriate, place to take a child--even on the Terrace. The OP indicated she was bringing a child with her. The waits are long, even if you have a rezzie, and the last time I was there I didn't see a child's menu. There are dozens of child-friendly restaurants within a few minutes' driving. Save George's for a kid-free evening.

If you want a child okay restaurant in La Jolla, The Cottage one street off Girard is nice (and has outdoor seating). Harry's Coffee Shop is great for lunch/breakfast - on Girard.

Sorry. mahlquist, but I cannot see where the OP says she will have a child with her.

I really do not agree that George's Terrace is expensive, not at all.

http://www.georgesatthecove.com/ocean-terrace/menu.php