I love this handy dandy little app. What GoodMerge does is take all similar games from your Good sets and compresses them into a single archive using Zip, Rar, 7-Zip or Ace.
For example, The 2614 N64 games are compressed into 393 achives each containing only different variants of the same game. The benifits of this are better compression and organization. When used with 7-Zip on larger Good sets such as GBA, N64, SNES, ect. you get unbelievable compression
(See the GoodMerge website for stats).
At the request of the author, the download link now takes you to GoodMerge's website.