For the three nights total we were in San Jose, we didn't end up doing much in the city. We were only there for two half-days and one full day, in which we went to our ziplining tour. We ate at two Peruvian restaurants and one Costa Rican restaurant, and made our own food in the hostel kitchen twice, one time accompanied by a very annoying guy who was still drunk from the night before...
We ended up walking around the city center a bit at night (which started aroun 6pm when it started to get dark). We visited a cute curio market where I bought some earrings. Instead of a cab back to the hostel one night, we decided to take the city bus, which ended up taking forever to even come! We got a lot of quality people-watching time in though :-)
It says "change the world"
Our last night in San Jose, we stayed in a hostel in the red-light district. We learned more about the area from a guy that drove us back from the car rental place to the city. You can read more about that here. Gonzalo was nervous to walk seven blocks from our hostel to Las Palmas, a Peruvian restaurant. It ended up being ok, but it was definitely a part of town where tourists weren't out bustling around after dark.
Overall, San Jose was not our favorite part of the trip, especially due to the rush-hour traffic we got stuck in more than once (one time while Gonzalo was driving). San Jose is probably worth at least a day, especially to check out the museums, which I heard were nice. We'll have to confirm that on our next trip to Costa Rica!