slashdot got this particular issue right (at least in the early 2000s, before their digg-envy took hold) by not awarding karma for anything modded up "Funny". while these "funny" comments -- usually brief and snarky or perverted -- would still appear +5, there was otherwise no long-term incentive. unfortunately there's no analogous control mechanism here (and copping slashdot's mod system altogether seems too heavyweight.)
there was also a karma cap (+50?) above which your comments would start out at 2 points instead of 1; otherwise there's little point in accumulating more karma than that.
their moderation faq is worth a read (skip about a third of the way down to "will you delete my comment?"): http://slashdot.org/faq/com-mod.shtml
also, some winding threads are really interesting (and vacuous ones are easy to skip) -- i don't know if it's worth the tradeoff to cull them.
(yes, i'm replying to the top-modded post so my comment goes above the fold.)