"Apple Extras" was / is a collection of utilities that came with the OS files - usually on a separate CD. It included the Airport admin utility, Sherlock, Universal Access and a bunch of other stuff. If you have it it would be a folder labeled as such. You can always download a complete OS9 package from our downloads section and get extras out of it.
Here's a thought: If the system on your computer seems to be incoherent to you, like too many previous folks have messed with everything so you can't really tell which way is up or down, you might be well advised to just scrap the entire OS9 install and reinstall a new one. That way, you know everything you need will be there in approximately the right places.