Collapsable threads might be a good idea, but I'd prefer having the system make its values explicit via descriptors for comments (think Slashdot or Plastic). My top two would be "insightful" and "uncharitable". The former encourages what's best about this community, the latter strongly discourages what's worst. A lot of deep and pointless threads are caused by commenters reacting to their own hasty interpretations of what someone said rather than even-handedly responding to them.

Also, no "Funny".

collapsible comment threads would be very much appreciated.

I've seen that work really well on a couple sites. I played a certain MMO for a while (I know, I know) and the overall maturity level was, shall we say...low. Anyway, one of the popular database sites implemented that feature for it's threaded comments and if you compared the tone of the discourse their to the tone on the regular forums, it was night and day. The trolls simply branched off into threads that where below a certain threshold and were autocollapsed. You could still see the parent thread title inline and click through to the full thread if you wanted, but the signal to noise was much improved.

word. i'm one of the standard slashdot->proggit->hn users. slashdot's comment system rocks (ui and concept). it's a very strange worse-is-better effect that reddit and hn have both meant losing features in exchange for the advantages of being part of smaller communities.

edit: i was going to whip out a greasemonkey script to do just that, but then i saw that the comments are just one big table...ug. i was hoping for nested div's. eit.