I've figured out the format of the files eq uses for achievements and wrote a python program to generate showeq filter files. There's almost 400 zones, so it's possible I may have gotten the zone names wrong, but I think I got most of them correct.
I'm posting 3 zip files with the filters. Unpack and then drop the *.xml files into your showeq filters directory (~/.showeq/filters for me). If you are already using filter files, you'll probably want to merge your files with these. Note that these files only contain mob names that are on the Hunter achievement lists; other mobs (quest mobs, raid mobs, etc) aren't in here.
I'm also posting the python program used to generate the files, get_hunter.py. If you grok python, feel free to dig around in it, make changes and whatever. You'll need to have your windows everquest directory mounted somehow on your unix box.
The xml files are formatted so it's easy to remove a mob once you've gotten the checkmark, just edit the filter file from within showeq and delete the relevant line. Then reload the filter and it will no longer highlight that particular mob.