Here's a list of things you can visit and do while in San Diego for Comic-Con. I'm not going to include the obvious and most popular tourist destinations, such as the "World Famous" San Diego Zoo, museums in Balboa Park,. Instead, I'll provide a list of cool things to do and see that may not be listed in your tour guide.
 
1. Kansas City BBQ
The coolest thing by far (well, I think so)... is something that very, very few San Diego locals even know about and it's only 5-10 mins walk from SDCC. For about the same distance of walking and same price, you can eat somewhere that's a part of history. DO YOU FEEL THE NEED - THE NEED FOR SPEED?
 
If you know the famous movie where that quote is from, then you'll remember the bar scene where Maverick (Tom Cruise) is singing and Goose is playing the piano. The piano and bar is just across the street from the convention center. There's virtually no parking there, so it's much easier to just walk there for lunch or dinner from the convention.  The actual Top Gun school has moved out of the area (about a decade or so ago to much further north in northern Nevada), but most of the places shot for the movie is still around town.
 
2. Coronado Ferry ride
Coronado Island ferries leave about every hour from the San Diego Harbor/Embarkadero. It's about a 30 minute ride across the bay to the City of Coronado - that's the "island" that you can see from the back of the SDCC where the big arching bridge goes to. It's about $7 for a round trip ticket. Once you've landed in the Coronado side, there's a few restaurants and sights to see. If you need a break from downtown and want to have dinner close by, then you can enjoy the view and take a ride out to Coronado and back. The ferry landing is just north of Sea Port Village and walking distance ( about 15-20 minutes) from San Diego Convention Center.
 
3. USS Midway
If  you've walked to the Harbor area (north of Seaport Village), then you can't miss the USS Midway. It's a large US Navy aircraft carrier where you can take a tour. The hours are 10-5 (last tour starts at 4pm). It's a nice tour, but a bit costly - about $20 per adult. It's also walking distance ( about 15 mins) from SDCC.
 
4. San Diego Maritime Museum (Russian B-39 Submarine, Star of India)
You can take a tour of an Russian B-39 submarine, an US Sub, the Star of India (built in 1863), and another sailing ship. There's also an historic bay cruise. Even if you don't want to pay to see the insides of the ship, you can walk right next to them at the harbor. It's about a 25 minute walk from SDCC. 
 
5. Seaport Village 
This is the small section of shops directly behind the convention center and hotels. It's much closer and easier to get to (and there's trees/shade there) compared to Gas Lamp district where everyone at the convention will be eating lunch at. Seaport Village has a few restaurants, a "food court" area, and lots of shops. It's 0.5 miles from the SDCC, about 5 mins walking and you get to walk along the coastline without dealing with cross streets and traffic.
 
below items need car or other means of transportation (such as trolley)
  
6. Hotel Del Coronado and beach (need a car or take multiple transportation means)
The hotel is one of the oldest in San Diego (if not the oldest). It was featured in movies with Marilyn Monroe (free Marilyn Monroe exhibit) and the likes. There's a bar, coffee shop, grill on the outside deck, and a very expensive restaurant within the hotel (along with some shops). I believe the real gem is the beach behind the hotel. I believe this is one of the better beaches in downtown San Diego area. It's not too crowded and not as touristy as Mission Beach. To get there, you can drive over the Coronado Bridge (it's the big arching one, and the one where the dog got thrown off in Anchor Man movie) or you can take the Ferry (see above) and a pedi-cab ( or walk about 1.5 miles from ferry landing). Rumors suggest that Orange Ave (the main road going through Coronado) inspired the "Yellow Brick Road" and Hotel Del was used as inspiration for Emerald City in the Wizard of Oz (writer wrote some of the original books there).
 
7. Old Town San Diego
You can take the trolley and a short 5 minute walk from the Old Town trolley stop, a taxi, bus, or even hop on a tour trolley car (pay them) (the non-public transportation trolley cars that look like the ones from San Francisco, commercially operated for city tours). While there, walk down San Diego Avenue for a bunch of decent/good Mexican restaurants and margaritas. There's a famous haunted house and a few cemeteries along the way. There are also some shows (of old Spanish/Mexican dancing and such), lots of shops, and lots of city tours offered from there.
 
8. Mission San Diego (popular tourist site, need a car or taxi)
I've never been here, but it has a great view of Mission Valley - be sure to go before the sun completely sets.
 
9. La Jolla, Children's Pool and La Jolla Cove  (requires car or taxi)
This is about 30 minutes away from downtown. You can park and walk towards the Children's Pool to see live/real seals. This is the controversial beach that was owned by someone and was a "seal beach" until they died and gave it to the city. Now local residents want it to be used for children and to drive/keep away the seals - which many locals want the seals to continue using it. It's been in the court system for decades now. The area where the seals are located is roped off, so don't get too close - they will attack you (the seals and maybe locals if you try to cross the rope :) ). 
 
There's a nice park  there and you can walk down along the other shorelines. At the cove, you can kayak, swim, and snorkel. If you're heading to the convention and your family wants a day adventure without out... then they can easily spend a day here for free (excluding parking and whatever they purchase). There's also a hidden sea tunnel that goes out to the ocean found beneath an old store ( La Jolla Cave Store). It's easy to drive past the Cave Store, so look it up via online maps. It costs a few dollars to walk down there and the steps are slippery, but the view is pretty good (check out photos online).
 
P.S. it's pronounced "La Hoya" (it's Spanish, don't pronounce it like it's spelled). The "ll" make a "y" sound and the "J" makes a "H" sound.

10. Tijuana, Mexico (can drive and park car on his side of border or take trolley or taxi, don't recommend driving into Mexico - most rental agreements forbid it)
If you're adventurous, you can head down to Tijuana (or "TJ" as we call it). You can head in and have a drink at the Hard Rock Cafe and return to check off Mexico from your to do list - be sure to bring your passport. This would probably be a half-day to full day adventure, so plan accordingly. TJ is about 20 miles south of San Diego. 

Yeah Kansas City BBQ is awesome. I go there when I'm in San Diego every year, at least a couple times. We have great BBQ in Florida, but nothing like that.

10. Tijuana, Mexico (can drive and park car on his side of border or take trolley or taxi, don't recommend driving into Mexico - most rental agreements forbid it)
If you're adventurous, you can head down to Tijuana (or "TJ" as we call it). You can head in and have a drink at the Hard Rock Cafe and return to check off Mexico from your to do list - be sure to bring your passport. This would probably be a half-day to full day adventure, so plan accordingly. TJ is about 20 miles south of San Diego.

great list ;)