There are probably a lot of programs that do this, but the one I know works is MPEG Streamclip-
http://www.squared5.com/svideo/mpeg-streamclip-win.htmlIt's for Windows and Mac. It's a free program designed to help edit video files (compared to converting them), but it can do some a few other things as well. What you would want is for the file to be (or turn it into) a kind of un-compressed video (MPEG, MPG, VOB, DV) instead of a kind of compressed video (MP4, AVI), then rotate and re-export the video.
One negative of this method is that it requires uncompressed video, and it requires either Quicktime or Quicktime Alternative.
...actually nevermind with that. Here's some suggestions that probably use software already on your computer-
http://www.makeuseof.com/tag/rotate-video-files-mac-pc/