So here, in no particular order, are the features you've asked for, plus some that I've been thinking about. The likelihood is all or most of these will eventually be implemented. But I'm concerned with what to do first. What do you want to see?
1) Comment Moderation
A perennial standby. Comment scoring by you, the readers. This, of course, brings along with it all the bagagge of thresholds, karma, and the question of who moderates. Or does it? If this is important to you, what parts of comment moderation should we keep, if not all of it?
Everybody likes polls. I like polls. I'm sure you do too.
3) More Searching Capability
Search for users, stories, authors, free-text, what have you. All the nice site searching stuff.
4) User Diaries
This might be totally out of left field for most of you. There's a site called Advogato that has a little thing whereby any registered user can keep and update a personal "diary." Implemented here, there'd be some kind of "Recent Diaries" box on the front page, listing recent updates. You'd also be able to search or browse users and check out their diaries. I think this is a cool feature, and I'm not above shamelessly copying it.
Much like polls, everybody likes themes. The general idea is that you could pick a predefined theme, or create one of your own, and probably submit it to be evaluated as a site-wide predefined theme as well. This is doable, since almost all the colors, fonts, layout, etc, are being grabbed from the database on each page load anyway.
6) More Extensive Story Filtering
hattig suggested that perhaps there could be a way to tag stories as "mostly" of interest to certain nations, perhaps even to select only to display stories in certain languages. I think internationalization is cool.
7) More Boxes
You'll note there's not much in the way of "boxes" right now. I've been thinking about making a general rdf parser for the standard my.netscape backends, and an easy way to add and administer portal-style boxes, that get content from other sites. Also, I guess there'd be a way for users to select what boxes they want to see, and order them and stuff.
Ok, I'm sure there's something I've boneheadedly forgotten. If something should really be on this list and it ain't, mention it below and I'll add it.
Now don't hold back. You've all been so timid about telling me what I should do. ;-) Tell me how you really feel.