ffmpeg -i in.mov -vf "transpose=1" out.mov
For the transpose parameter you can pass:
0
= 90 Counter Clockwise and Vertical Flip (default)1
= 90 Clockwise2
= 90 Counter Clockwise3
= 90 Clockwise and Vertical Flip
Use -vf "transpose=2,transpose=2"
for 180 degrees.