I remember reading about something like this before but don't remember where or when.

Basically I was thinking about people that don't have the RTP and/or didn't want to bother downloading it, so I figured it's easier to just deliver the game with those files as well.

But then chances are, if it's a small game, 80% of the stuff won't be used.. Actually I guess even in large games, most of the resources may not be used.

What kind tools are there for this?

Yeyinde's Data Checker. It will indicate you which resources are used and which aren't, so you can clean up.

Looks interesting.
Does it compile a nice list of files so I can just pass it to another script that will walk through my folders and do the clean-up for me?

No, it indicates you in a message box the potentially unused files (by unused, I mean not used on the editor - files used in scripts can be flagged as unused too sadly) and you have to go through the trouble to delete them yourself.
Yeah, you'll have a bit of work to do yourself, I'm afraid.