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".