I spent a week down there in 2000 and had a blast. I would advise traveling to and staying in some of the smaller towns/villages near either coast (if you email me I can get out a map and tell you the names). There are some cool rain forests, a volcano, and even a bar where you can feed monkeys bananas. Oh yeah and of course topless beaches. Whatever you do don't bum around San Jose - get out to the inner part of the country and the coast!
If you do have to stay in San Jose, I would recommend the Grand Hotel Costa Rica. It is an old hotel in the downtown cultural district. You can book numerous tours/activities from there. I did whitewater rafting on the Reventazon (sp?) river and had a blast. Also did horseback riding in a rain forest. If you want more details, send a PM and I'll reply. Lots of cool things to do all over the country.
I hear the volcano is a really neat thing . I also heard through the grape vine you can get some real cheap companionship for a whole weekend. A gorgeous chica that cooks, cleans and does a lot of mmmmmm. housework. I am in no way condoning that type of thing but it is a fact of life in that area .