Thanks for the suggestions. Either way there's a lot of work I'll have to do by hand. To keep my library clean, I think the best approach would be for me to manually enter each game's region and missing metadata.
One suggestion for a future version would be to automatically fill each game's metadata according to its filename (title or checksum), depending on the nomenclature the user chooses (GoodMerge, No-Intro, TOSEC, etc).
Or better yet, try to match the name with one of the many existing rom info databases, like this: http://emumovies.com/forums/files/file/607-system-ini-files, instead of connecting to TheGamesDB, which is very incomplete.
This would save a lot of time to collectors who own full rom sets.