Personally, I make HEAVY use of OS X services to send things to the right inboxes. Using Evernote's clipper (well, actually the
custom services I built to replace the clipper) and OmniFocus's clippings or send-to-inbox service, I can shunt information from any app into the right "inbox."
I use the same tools to move items between apps as well. Select text in Evernote, then "Send to Inbox" and I've got a task waiting for me. If I have a lengthy note I clipped from a website into OmniFocus, I can select it and send it to my default notebook in Evernote.
This does mean that I have an extra inbox to sort, because there's no automatic tagging or anything in there, but it sure does get the job done, quickly and painlessly.
ReQall would be easy enough to include in this workflow, by just selecting the text in your browser and sending it along with the right keyboard shortcut. Just another inbox.