I read that you’re manually tagging them, so your process can be whatever you want to do.
For example, you can leave the images in their current folder structure and create a separate folder structure with symbolic links to an image, so in the character folder would be symbolic links to all the images like that. They also don’t have to be unique, an image can be in multiple categories.
Alternatively you can use a spreadsheet and generate lists there.
Finally there are plenty of photo album applications that allow you to tag images.
Wow!
I’m guessing that WordPress will be forked soon …