DOSOrganizer - use this tool to help sort your games.

This is a windows app, pretty self explanitory.
1) Point it to the big list o' games are located
2) Select the type of sorting you want (year, alphabetical, publisher, genre)
3) hit Move Files!

All files will be moved into a folder below whereever your main directory is.
It'll create an undomove.bat file to move everything back if you ever want to.

Bug/Note:
Files that use extended ascii characters, such as anything by "Brøderbund Software, Inc." may fail to be unmoved using the batch file.  
Win2k seems to be more sensitive to this than XP.  I'm not going to touch Vista, so good luck there. 
This sucks, but I don't have a solution, or at least not enough time to come up with one.  maybe next time.
The folders that DOSOrganizer creates are also not deleted after restoring all the files.  I'd suggest highlighting them all, check properties for files size, and if everything is 0 bytes, then delete 'em.