Found this thread over at the video related forum. Gist of what I gather is you need to re-encode the video, losing some (possibly unnoticeable) quality in the process. You can use player software to playback correctly rotated, but you would have to do it everytime you played the video. VLC player can do rotate in this case.
NOTE: The thread is over a year old, so there might be a better way now, this was just the first good result I found hitting up google.
SMPlayer is another free video player that will let you rotate or flip the video. I had been using VLC, but I like SMPlayer much more. The option in SMPlayer to rotate or flip is so easy to access that it takes about one or two seconds to find and access it. Also, SMPlayer will remember the settings you used for playback of 'x' number of videos [I don't remember how large 'x' is]
As far as reencoding and rotating at the same time, during my limited experience with using some of the free video encoders here are two more options that I don't think were mentioned in that videohelp thread that you cited:
AviDemux and Format Factory
AviDemux is so feature rich that it's a little overwhelming, while Format Factory has a smaller learning curve. I'd describe the differences between the two of them in the extensiveness of features as being like Microsoft WordPad versus Microsoft Word.
Virtualdub, which is mentioned in the thread you cited, is sooooooooo loaded with features and options that it blew my mind and I gave up on trying to use it for encoding and rotating/flipping.