Most importantly, make downvoting cost one karma point per downvote.
if you have a way for people to flag what they think is bad stuff, you don't have to moderate every comment (a la boingboing and others) and you don't give people a free-for-all. additionally, it allows a user culture for the site to emerge as a collective tone is carved through the kinds of posts that get removed or downvoted.
this is a big thing. i think a lot of sites are jumping on the no-anonymity bandwagon because that's what third-party commenting sites push in order to pump up (i'm speculating) registration numbers. disqus allows (or allowed at the beginning) anonymous commenting, but i haven't seen any site that uses disqus to allow it.
i think this is a market failure. i saw third-party commenting as a way for sites to no longer have to implement their own user registration facilities regardless of whether they allowed anonymous commenting. they just figure hey, we can have our bloggers be able to log in, keep that part simple, and then throw the rabble to disqus for them to deal with. typically i've found this causes the commenting culture to shrink a great deal.
i think there's space for a third-party comment provider to allow arbitrary name/email(will not be shown)-type anonymity, while still implementing flagging, voting/karma and, perhaps most-importantly, IP-banning. it wouldn't be perfect, but i do think it would allow more freedom on both sides: to comment, and to be (more) free of moderation overhead.
Which would mean that your comment wouldn't be allowed as your account was created two hours ago ;)
similar reason I don't contribute on SO... I don't have anything to prove, I might have wanted to share some help, but I don't need to waste my time jumping through their hoops and silly badge games to contribute.