VirtualDub (.com) has a video filter that does a just-fine job of rotating video. It's a Windows app, though, and I can't recall what you're running these days. It's super-useful handler and basic editor for any .avi. Also, what format are you using? It's usually not so much a matter of format but codec, where nearly all PCs ship without a lot of popular video codecs. If you're referring to flv files, well, yeah, it's not popular with video players. Ditto tne relatively new MKV.
Oh, huh.
Actually yeah I clipped this with VideoDubMod, some variant of that.
You still have the issue of Youtube being in landscape mode, however.
And yeah, Canon cameras still use this weird MJPEG format for movies that tend to be annoying to view.