Do you mean rotation on playback or converting it to a rotated version?
As a commandline-user I normally use mplayer:
mplayer -vf rotate=1 videofile.mp4
(rotate can have values from 0 to 7, 1 rotates 90deg clockwise)
Convert (requires transcoding):
mencoder -vf rotate=1 videofile.mp4 -oac copy -of lavf -lavfopts format=mp4 -ovc lavc -lavcopts vcodec=mpeg4 -o newfilename.mp4
(you can use other video codecs as well, this is just an example)
And here is a graphical tool to do the latter: kdenlive (a kde application from the universe)
- import your video as a clip
- draw the clip into the timeline
- rightclick onto the video chunk in timeline
- select "Add Effect" -> "Crop and Transform" -> "Rotate (Keyframable)"
- The effect can be configured in the upper central section of the window, set X to 900 (thats 90 deg clockwise)
- Render your project (Project -> Render in the main menu)
- Be careful to choose a video resolution for the resulting portrait format
- select any video codec you like, i recommend x264 or vp8 (webm)