Off the top of my head:

• Stop showing user page edits in the LW wiki sidebar.
• Also in the sidebar: Don't show reverted edits to pages. Show the last real pages with non-reverted edits.
• When a moderator deletes a comment, if it has no subcomments or if all comments have been deleted, don't show any leftover traces. If there are subcomments, require a deliberate user click to expand them and only allow logged-in users with >=1 karma to do so. Apply the -5 karma troll toll to comments with a deleted ancestor.
• Show parent comments in user comment feeds (the list of a user's most recent comments). If the user has less than 80% upvotes, enable downvoting in the comment feed for users with over 1000 karma.
• Cause new comments on a post to stand out more than they do currently (the small green aura does not enable super-easy scanning).
• Implement Reddit's "highlight comments since..." feature.
• Show the most recent Rational Quote comment in the main sidebar, the most recent Open Thread and Rationality Diary comment in the Discussion sidebar (i.e., the latest comment from the latest post with the appropriate tag).
• Automatically strip crap (the sort of stuff e.g. Word generates, but all text editors seem to do it now) from the post editor.

More ambitious projects:

• Easier tracking of ongoing discussions - "subscribe" to a post and see new comments on it forever, possibly in a separate inbox.
• Subreddits besides Discussion.