I have both.
For ongoing arrangements that involve a large amount of shared commitments with the person or topic, they each have their own "agenda" file or list that includes what I'm waiting for from them, but also includes things they are waiting for me on if they aren't time sensitive, (i.e. my husband, accountability partner, group work collaboration, good friends, etc.). The one off deferred actions (waiting for test results, waiting for feedback about birthday party, waiting for hotel to get back to me for the holiday we're taking in December, etc.) go on a general waiting for list.
I also update it regularly. If the agenda hasn't been used in a while or is only used sporadically, then that person or topic gets moved to my general list. If one topic is dominating the general list, it gets its own agenda.
Upon reflecting, I do the same with the organisation of my projects too. I have a projects section of my filing cabinet for the big stuff, with each major project getting its own folder. Then I have a folder at the beginning of the same section filled with the all of my mini projects that only have a few steps.
It definitely keeps the one offs from getting lost and the big stuff from getting jumbled, that's for sure! The secret is, as with many things in GTD, in the Weekly Review. I know that I will be reviewing the content and structure of the content once a week so nothing ever gets to the point of becoming ridiculous or overwhelming.
Ha. I was about to say, "It's a fluid process.". Then I remembered Dave's, "Mind like water." ... Now I get it on an even deeper level. Genius.