I have a solution for you, use
MPlayer. There are versions for Windows, Macs and Linux. But you'll need to use the command line rather than a GUI interface.
Code:
mplayer -vo gif89a -ao null -ss hh:mm:ss -endpos nn some-video-file
This command will start at hh:mm:ss and run for nn seconds. The output will be stored as an animated GIF called out.gif in the current directory. My avatar of Yukio-chan was created in this fashion.
You'll still have to edit it with a program that supports individual layers. I use the
GIMP.
If you use "-vo jpeg" you'll get a sequence of individual JPEG images numbered from 00000001.jpg through nnnnnnnn.jpg depending on the length of sequence you're capturing.