If you dont mind paying ...
Adobe Premiere Elements, Nero Vision are couple that are very good for this sort of thing.
Both go beyond just adding a audio track though, allowing cutting/editing, PiP, and special effects. Adobe being the superior of the two, and my personal recommendation.
Theres also Sonys Vegas, but I havent used it much so will not comment about it other than I hear good things about it as well.
For free, Windows is really the only one I know of right off hand myself thats decent, and its quite cripple compared to the paid movie makers. But its free vs paid software so it stands to reason.
Most apps that covert or compress, such as Handbrake, MeGUI etc (2 of the best H264 encoders BTW) are just that, encoders. They are really only good for recoding to a different format and compressing to a smaller size.
I/E use a movie maker to make your movie and save as a full quality DVD, or very high quilaty file. Then use the encoder to compress those very large files to a MP4 file for youtube for example.
If you are serious about making/editing your own movies, and do so often, It would be a worthwhile investment to buy one of the paid applications. They are superior in many ways. Not only in what you can do, but the final quality as well.
If you want to stick to free perhaps others have some good suggestions for you.