I am looking for a unix (freebsd compatible) command line tool to
extra thumbnails out of different kind of movie clips like ImageMagick
and other tools can do with pictures (example: one thumbnail every 10
seconds). The tool has to support the main video codecs (WMV/MPEG) but
more codecs/libraries would be prefered (ex. DiVX, XVID etc). I was
searching for links to open-source projects which can handle this but
couldn't find anything yet.

It is important that has to be a command line tool to support batch
processing and that no X-windows is available.

The transcode utility can do what you are looking for.  This can be
built from /usr/ports/multimedia/transcode.  Make sure you review your
make options (WITH_DIVX5=yes as an example) before you build.

Once you have transcode installed, you can use it to extract images
from your video stream like this:

transcode -o outputfile.jpg -i inputfile.avi -c 2100-2101,4544-4545 \
-y jpg,null -Z 320x240 -z 

This command will save frames 2100 and 4544 from the inputfile.avi
video into jpg files of size 320x240 named outputfile.jpg000000.jpg
and outputfile.jpg000001.jpg.

An explanation of the options:

-o            the base output filename to use
-i            the input file
-c            the frames to decode
-y jpg,null   sets output to jpg for video, null for audio
-Z 320x240    resizes the image to 320x240
-z            flips video horizontally

If the faces appear blue, swap the red and blue channels with -k.

You can also output to .ppm and a few other file formats described in the man page.