I ran into an issue where I had a bunch of large (full page size) images with lots of little images that I wanted to use for tokens within them. So that I wouldn't go insane I put together this python-fu script for Gimp 2.6 which does 99% of the work.
<a href="https://www.dropbox.com/s/zaiah2liql7gh38/create_token.py" rel="nofollow">https://www.dropbox.com/s/zaiah2liql7gh38/create_token.py</a>
To use:
Stick the script linked above in ~/.gimp-2.6/plug-ins/
Start Gimp
Open your large image
Select the area you want to use as a token (needs to have a consistent background color)
Go to the "My Scripts > Create Token" menu
Enter the file name
Hit OK
The script will create a new image from the selection, autocrop it to fit the actual token and replace the background with a 50% transparent white fill.