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
-vf "transpose=2,transpose=2" for 180 degrees.
Make sure you use a recent ffmpeg version from here (a static build will work fine).
Note that this will re-encode the audio and video parts. You can usually copy the audio without touching it, by using
-c:a copy. To change the video quality, set the bitrate (for example with
-b:v 1M) or have a look at the H.264 encoding guide if you want VBR options.