I ran the 5k race in 2012 at the Balboa Pier. The Marines are all over the course helping and encouraging everyone. The whole thing is organized with military precision. The obstacles are very challenging and the 5k felt more like a 10k. To me, the most difficult challenge is the litter drag, and the best part was the encouragement of the Marines. One of them that had already raced ran with me for the last 100yards to push me to finish strong. After the race you can chat with the guys and check out the military vehicles they bring down as well as grab some swag from the vendors.
This year they changed the venue to the Dunes Resort and the 5k is on a lot of asphalt. I prefer sand so the 2k might be a better bet for me this year.