Slashdot (the pioneer in this sort of moderation) has always had a 'reason code' for up and down votes (and meta-moderation to check that the reason codes are good).
This allows you to do things like filter results to only high scores, excluding 'funny'.
Even just separate buttons for "funny" and "informative/insightful" would be pretty nice on reddit or HN.
Slashdot's comment moderation system always seemed to work pretty well to me. The general editorial quality is what made me give up on them. (When I checked back recently, most submissions were incredibly blatant flamebait.)
i actually gave up on slashdot because the comment system had a very clunky feel to it, to the extent that it made the site offputting to use. i likewise do not participate on the making light boards, for the same reason, even though in both cases the actual quality of the discussion is excellent. reddit has nailed that aspect.
This allows you to do things like filter results to only high scores, excluding 'funny'.