As someone previously mentioned Sandeman's New Jerusalem Tour, I would recommend it. I personally haven't done that tour, but have done the same company's tours in Paris and Dublin(?) and they were great. They're free tours, and are really just highlights. So what we did on the tour is we'd do the tour, see a little bit of everything, get some history, etc and then we'd note the one's we really liked and go back and visit them in detail after. On the one's I did, we generally didn't enter the places on the tour, just stood outside and learned about it. So, assuming all is the same in Jerusalem, I'd recommend it. I also live in Israel, so I know that the itinerary they have is solid.