I noticed a several people suggesting features in other threads, so I'm starting one explicitly for that. I know there's a lot that needs improving; the site is pretty bare-bones at this stage. So propose whatever new features you think we need, and vote for the ones that you want most.
This is more a content issue but to really build the community is have more fully fledged profiles - with location, bio - make it one or two lines max and a website or blog link. If we are what we think/read then it would be a great starting point in finding cofounders or people who are on the same wavelength.
I would also agree on seeing the latest comments - and maybe highlighting posts which you've commented on/ or submitted showing if there were new comments that you haven't read. So show "7 comments | 3 new" so it would be easy to come back to your home page and see how the discussion has evolved.
More important, I think, than displaying the number of new comments is making it possible to /find/ them. The reordering of comments is usually a great thing, but in a relatively involved discussion, it can become quite a chore to find that new comment.
I'm not sure what the best way to implement it would be, from either an algorithmic or HCI standpoint, but it certainly would be nice if you could come up with a way to make new comments stand out in threads. (Preferably with new defined by when the user last viewed the page, rather than being a static global definition.)
I find myself marking up comments of the same 2 or 3 users more often than others. They don't have ultra-high karma or anything- they just are interested in the same articles and discussions I am. It would be nice to learn more about them.