Better moderation in submissions and comments is probably on top of my list.

Hacker News has a high minimum quality to its comments and an O.K. maximum quality.

It annoys me that no distinction is made between users. I'd like to have something to let me know who I am talking to: a "friend and foe" list, and something to set users in comments apart such as coloured names, non-hideous gravatars, etc.

I'd also like special people's names to be highlighted such as the OP's and admin's. And a better voting system. And a pony.

Could you link to a Twitter account, e-mail subscription of some sort? There's a 95% chance that I forget everything you just wrote after I close this tab, unless Techcrunch, Daring Fireball, and HN shower you with attention.

EDIT: If you want a good case study to learn from, see how Quora has failed to shape and teach its users how to use the service and post relevant, good content

EDIT2: A "report" button for individual comments would also be great. Moderators can't be everywhere; instead, they should just teach users to (properly) report comments and sift through these. It would also be beneficial to require a description of the infraction.