This is more of a UI/UX question, but I thought about it on and off for months and have a partial answer. Look at how Gmail works - you have All Mail, but you also have Inbox, Sent, and your own custom labels (tags). Every message can always be found in All Mail, and you can restrict your search by date range. Similarly on an image board like Danbooru, even if you don't tag an image, it will appear on the chronological stream of every image ever uploaded to the system. So, I'm hoping the design will end up something like these two examples. You should be able to list every file, preferably in chronological order; you should also be able to exclude files that have at least one tag; and the software might have a special nag section showing you all the files that you left uncategorized.