What works

Basically everything

Searching through the catalog

Opening up *.afo files (see What does not work, below)

Adding to the catalog (except some hard drive partitions/files may not work, '/' on ext3, etc?, links? - not really tested)

Saving the catalog

Going through the catalog
(except for the few folder that might crash it)

Getting file/folder properties

What does not

Deleting the last item in the catalog will crash it
Opening a new *.afo or starting a new *.afo with one open will crash it
(upon the closing of the old one? see above)

Workaround:
Close Advanced File Organizer
Move or rename the current *.afo file
Restart Advanced File Organizer and then
Open the new *.afo file

Open in Explorer for stuff from older computer setup
(probably not Wine's fault)

Opening a folder may crash it, but that isn't that common?
(This might happen more if you're going fast? or with a specific folder, or path? why?)

Might not be able to scan some non NTFS/FAT hard drive partitions files/folders?
(I don't think the program was designed to do that, and I didn't fully test, somehow I got the Linux folders on there, but I think I was using Windows and a program that allows access to EXT3 through Windows, instead of Wine. Could I use that program in Wine to get it to work?)

In Find, button must be pressed instead of the enter key or button

Icons flash when the mouse goes over them

What was not tested
Messing with 'Open in Explorer',
and how to work around problems
(if possible)

Figuring out add to catalog restrictions
(can you do '/' on ext3?, etc...)

Additional Comments

I recommend saving any new *.afo s as a new file and saving the old windows one as a backup.
(No problems yet with this, but as a just in case safety precaution)