When reading the replies, it seems that there is not just one succesfull formula.
For me, it works best to have all my "Waiting for" on one list (I use RTM as a list manager), so when I do a review of this list, I have them all in one place.
However, I keep a copy of the e-mail for which I expect a reply in a @Waiting for folder, so when I notice in my weekly review I have not received a reply to my e-mail, I have all my open WF e-mails in one place and do not have to look into my reference archive. I find this way much quicker.
I have set up my Outlook to automatically move a copy into the @waiting for folder. I have set up a rule in Outlook when I ad WF to an e-mail (I do this in the bottom of an e-mail in a small font so the receiver cannot see it), it automaticaly moves a copy to mey €watiting for folder.
Hope this helps