I have had these small wart-like bumps on the base of the shaft of my penis for many years now (2 on left and 2 on right side). They have never bothered me or gotten worse, and I have had physicals where my doctor has just glanced at them, but hasn't said anything about them. I just figured they may be a result of me shaving down there, but I wouldn't think they would be permanent like this. Any ideas?

It could be one of several things. If you are thinking that they may be genital warts(HPV), try this home test:How Vinegar Is Used To Diagnose Genital Warts

The best thing for you to do is to go back to your doctor and talk to her/him about them.