I have a Waiting For folder that I use to store the single items that don't have a project but are related to a WF item. I also use it as a "quick find" area for those items that I don't want to put into reference. Eg. I have receipts from credit card usage that I must log for work purposes - the card is used regularly and it is much easier to leave a colour plastic folder in my WF support which I can find quickly and easily when I have something to add to the file. The file sits on my desk so it is quick to hand.
If you feel that you would prefer to keep things in a reference or project file that is no problem - create the system to suit your needs and way of working.
Hope this is helpful.