A rotate filter was recently added to FFmpeg, which allows rotation by an arbitrary angle. To use it, you can build the lastest version from git or download a recent snapshot build.
The angle is specified in radians; positive is clockwise and negative is counterclockwise. If you have degrees, multiply by PI/180 to convert to radians. For example, to rotate 3° counterclockwise:
ffmpeg -i in.mp4 -vf "rotate=-3*PI/180" out.mp4
Check out the documentation for more details and additional examples.
