There's also usually a "Master" wave for meta-discussions and overall project coordination as well as final assembly.
Waves are generally setup with a header "wavelet" we use for channel meta-data/notifications/schedules and such, so they don't get buried down in the wave someplace. Everybody edits those, but in general the agreement is to pretty much just leave the waves you put in as-is and don't mess with anybody else's.
As often as not, if there are just documents, we just make it in google docs and link to the doc in the appropriate wave. We've found that's the best way to handle collaborative document editing. We haven't had a chance to take advantage of the new docs features yet, it probably would have saved us even more time since we had to export out the final document into MS-Word for final editing and insertion of various diagrams and such.
One thing that would be nice, now that we've done a few projects like this, is the ability to hierarchically organize groups of waves. Right now we have to be careful to name the waves well...like "Project 4459:Phase A" or some such and search for them.
It's completely replaced using groups for us and various other collaboration sources, the asset management is just much better since it ties the discussion and assets together. However, it would be nice to just have a list of attached files to scroll through sometimes. On our last project, which lasted about 14 weeks, we got everything done on-time with this, but with far less frustration, less problems with organization of stuff, only a small handful of emails (it would have easily been thousands of emails bouncing back and forth) and really very few face-to-face meetings considering.
By way of comparison, a similar project I worked on resulted in thousands of emails, twice weekly multi-hour in-person meetings, constant phone calls, and when summing up the work a mad dash to find lost project assets.
I felt like I could have done 3 or 4 projects simultaneously like this with all of the saved time instead of just one.
We also set up lots of one-to-one or one-to-few sidebar waves for private discussions.
Basically it's a meta-discussion organizer for artifact production for our projects.
This is how http://BraintrustHQ.com works. It also has a simpler user experience focused on making conversations productive and organized.
We stick with IRC for conversations and e-mail for the matters that take a little longer to resolve. This suits better because e-mail and IRC are open anyway for customer contact all day long.
We use one Wave per issue (requirement/feature/etc). The top of the Wave we try to keep current with everything that we have discussed - so the first post in the Wave is sort of like a Wiki, while the rest is the discussion that goes into the creation of that post. This means we can come back at a later date and see how we arrived at the decision(s).
Once we are happy with how the issue has been resolved we then transfer it into JIRA. We could use the JIRA Wave robot but our current approach is fine for now.
We do have a full Redmine install set up, but there are only two of us, so it tends to be overkill - "multiplayer notepad" is enough for most purposes at the moment.