Because San Jose is cheap and slightly seedy (prostitution and gambling are legal), you tend to meet some very interesting people in the bars. On my last night in the city, a friend and I met this huge American guy who was way over his limit. He virtually dragged us down to his table, and for the next hour veered from insulting me and hitting on my female friend to bursting out in tears ('I miss my mama SOOO MUCH BAAAAH!'). We ended up running for our lives when he went to the bathroom. It was fun in a "let's see how weird this can get" sort of way. Anyway, the bars can be a little strange at times, unless you leave the city center and find a place that the locals hang out in. Some friends and I found one (sorry, can't remember the name) that was actually pretty nice - we sat there for hours, danced, and made fun of Canadian pop stars (two of the girls were from Canada - c'mon, Glass Tiger? Bryan Adams?).
My best advice for nightlife is to ask a local (maybe someone at your hotel) where the locals go - it probably won't be in the city center, but you'll most likely enjoy it very much. Costa Ricans (Ticos for short) are friendly to a fault, and they love to have a good time...