This might not be the best way because it converts your file aswell, but it saves loading it into an editing app so it's relatively simple(ish)
you can do it in Virtualdub (free download from:
http://virtualdub.sourceforge.net/ ),
File>Open select your clip
Video>Filters go to rotate, then select 90 degrees left or right
Video>Compression Choose the codec you want to use,
File>Save As Avi
The codec you should use will depend on what you want the video for, divX or Xvid are good for the 'net or e-mail, DV is better for editing.
and you'll have a rotated video. You could also do it fairly simply in most Editing apps, but it'll involve more steps.
There could be abetter solution to this, someone will no doubt suggest it some time soon. Good Luck.