They aren't genital warts if you've had them since 2002. HPV would have cleared your system by now.
They could be skin tags, dematofibroma, or really, a host of other things that are totally normal, but to find out for sure, your doctor would have to take a look and perhaps biopsy them. There are lots of things that cause bumps on the penis, and many look alike, so testing is the only way to know for sure.
I have a flat tag on the side of my penis for 6+ years. Looks exactly like a wart would look. About 2mm wide. It has never changed, never got bigger, and no other spots have popped up. Wife never got any warts either. I have read other forums where people have had wart-like flat tags. So, don't worry. It's almost certainly not an STD.