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You can also use ffmpeg and the commandline (taken from Rotating videos with FFmpeg):

Rotate 90 clockwise:

ffmpeg -i in.mov -vf "transpose=1" out.mov

For the transpose parameter you can pass:

0 = 90CounterCLockwise and Vertical Flip (default) 

1 = 90Clockwise 

2 = 90CounterClockwise 

3 = 90Clockwise and Vertical Flip

And to flip it horizontally (ffmpeg documentation):

Flip the input video horizontally.

For example to horizontally flip the video in input with `ffmpeg':

ffmpeg -i in.avi -vf "hflip" out.avi

Nota bene

Older versions of Ubuntu supplied avconv instead of ffmpeg. In this case just change ffmpeg to avconv:

avconv -i in.mov -vf "transpose=1" out.mov

Do you mean rotation on playback or converting it to a rotated version?

As a commandline-user I normally use mplayer:

Playback:
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)

If you just want to view a movie in a different orientation, as of Totem 3.1.4 (in Raring 13.04 and beyond), there is a "rotation plugin" which you can turn on (edit/plugins), and then rotate e.g. via ctrl-r.

I think proper rotation should be automatic when there is rotation metadata, and I commented on a relevant Totem bug here: Bug 701950 – Iphone Movies

There are also ways to do this in mplayer (and to convert to a rotated movie with mencoder), e.g.

 mplayer -vf rotate file.mov

or

 mencoder file.mov -oac lavc -ovc x264 -vf rotate=1 -o file-rotated.mov

The best option (in my opinion!) is OpenShot, you simply follow these easy steps:

1. Start OpenShot


2. On the File Tab, Import the video file you need to rotate


3. Drag the imported video to the timeline field at the bottom (either one will do!).


4. Once the videoclip is in the timeline field, right click on it and choose rotate to
   the desired angle


5. Then on the File Tab choose Export video and set the prefered format and location
   to it!


6. And presto!! That's it

OpenShot crops the video when rotated from landscape to portrait. To compensate, I tried these steps and it worked. Hope it works for you too.

1. place video on a track, right click and select properties


2. Under videos tab, uncheck "maintain aspect ratio" and "stretch full screen"


3. Under videos tab, put 90 for rotating clockwise, or -90 to rotate anti-clockwise


4. Under Layout tab, decrease width % to lower value (say 70) for both "start of click" and "end of clip". This value should depend upon aspect ratio of shooting, so try accordingly. Mine was 16:9 and value of 70 was fine.

In this way, you would find the video least cropped and it should not be noticeable.

A simple tool that can also rotate is transmageddon. Install it with

sudo apt install transmageddon

then load your file into it and choose the rotation position