As a starting point for tracking down some concrete examples I looked at some of the popular forums packages (and news reader things).
Here are some examples of framed browsers for long threads:
google
and
gmane.
Gmane is nice since it tracks what you have read, and has a
collection of well chosen key shortcuts, but it does not let you
collapse threads at all.
I think we could take a google style sidebar nav (which is pretty easy
to implement) and use Morten's tree
menu to construct a collapsable tree menu (the code is BSD licensed so could be included
in OpenACS).
For reference here is what UBB looks like
Flat
and UBB threaded
And phpBB One thread
and One forum
The support forum for phpBB has something like 100,000 threads and
500k posts which gives you an idea of how many users of phpBB there
are. Sticky threads stay at the top of the front page and
announcements are present on all thread pages. The user profile pages
are good and presenting post count is useful I think. Another thing
to take away from phpBB is how nice some of the themes are.
And in the make your head explode category:
ezboard.
ezboard has a tremendous number of forums with giant numbers of posts,
and there are some useful ideas there, although obviously it's not
really intended to support serious persistent threaded discussions.
One of the best things to look at is kuro5hin
(sort of slashdot.org but with generally higher
quality discussions). posts are rated, can be presented threaded or
flat, they distinguish editorial versus topical posts (although
to be honest people mostly don't classify them properly).
If you set Display: "dynamic, threaded", you can see the expandable
and collapsable threads. I think this might be the closest to what
you are talking about for #3.