I'd suggest some kind of OTC anti-inflamatory, like alleve - and maybe cool it down a little (icepack or something). But I AM not a medical doctor.
But, if you knee keeps bothering you - definitely see a doc. Here's my story. I injured my knee running in 2000. It hurt like a bitch, but I just stopped running for a few weeks, and after it started feeling better, I gradually got back to running. I was able to run again with no real problems (5-6 miles a few times a week) but I kept feeling a slight twinge in it every once in a while - but it was fine otherwise.
Fast forward a bit over a year and a half - and it starts to hurt again, and I go see a doc. It turns out that the original injury tore the meniscus (sp.), and had I seen a doctor at the time, it would have been a trivial orthascopic procedure, and I would have had no loss of anything - and could have kept running forever. Because I THOUGHT it was okay, and kept running on it for 18 months, I was damaging it further every time I ran, and it was a much more serious knee surgery. AND, after the procedure, my surgeon told me in no uncertain terms that my running days were OVER - and I would get really bad arthritis in the knee pretty soon.
So my advice to anyone is to NOT think that a joint is fine just because you can use it again. If you feel something might be wrong, get it checked out before you damage it more.