Cabrillo national park is great.. The view is unreal. Old town has a lot of nice Mexican restaurants. Pacific beach area is also very nice. I went with my lady this past summer and loved it.
I also like Cabrillo - great views and you can check out the tide pools below.
Hotel Del Coronado is like stepping back in time a hundred years and is right on the beach. Further north of Coronado is where the Navy Seals train and you can often see them.
I'm a big fan of the Zoo esp the polar bears, the road with all the cats, sea lion show, gorilla's & monkey. Definitely do the gondola - it'll take you to the polar bears.
The Safari park up north is also fantastic but in a different way. The lions are great and the unirail trip is very fun. It will be very, very hot in August so I would keep that in mind. There are a few "water play" stations. The condors are also pretty cool.
Mission Bay has a old wooden roller coaster and a small, cheesy little amusement park. Not so great but my son loved it when he was younger. It's fun to watch the people ride the artificial wave. The boardwalk in Pacific Beach is pretty fun - great place for people watching.
A favorite of my son was the model train museum in Balboa park. He loved going there. The Imax theatre is also fun and it has a great science museum that you can visit if you see a movie there. The gym in balboa park usually has some high quality bb games going on. Its near the Aerospace museum and San Diego Hall of Champions - Bill Walton, Ted Williams, Marcus Allen etc. etc. etc. Fun for a sports fan.
La Jolla is a great spot for walking - the children's pool CTO mentioned is great place to always be able to see sea lions up close. The Crab Catcher has a nice champagne breakfast on Sundays with spectacular views. Taking a kayak tour of the caves is great fun. La Jolla shores a good beach for younger children. Torrey Pines is a great beach too and you can do a hike up the hill, into the state park, down to the beach and come back to the car along the beach along the cliffs.
Lego Land is great fun but mostly for younger kids - say under 12 at the most. I would not take kids older than that there. Sea World is a better choice. It has a water park, some good rides and all the creatures. Getting is the water with dolphins is very popular.
I'm not a fan of Old Town. Kinda cheesey but a good place for a Mexican meal. The Presidio golf course is a pitch and putt and appropriate for younger kids.
Do NOT go toTJ. It's not safe and as soon as you get there, you will wonder why you even wanted to go.
Also, if you feel a need to watch a few hundred hours of recorded UCONN games -bb or football, you can ring me up.