First off, a seconding to riceowlguy's request for a change to how replies to your comments are delt with, namely in that clicking on the link to the reply doesn't remove the reply from the list, only clicking the link to the story entry will.
Secondly, I'd love to see an option by which both 'replies' and watchlist diaries are listed at the same time. Typically, I switch only between these two functions, and do so repeatedly throughout the day. Vertical space seems not to be a limiting factor in marginalizing this feature. What I'm imagining is a checkbox list of options in the user preference page akin to the feed subscriptions that says 'display the following: hotlist, diaries, stories, replies' with the function that any of those clicked would display on the page, as opposed to switching between options. This might have the advantage of diminishing the load on the server, as the data is called once from the server to draw the whole page, as opposed to twice.
Thirdly, rusty's recent comment regarding a 'watchlist page' for diaries gets a big thumbs up.
I have a few other requests, but they stem even moreso from laziness on my end than the above requests, so I'll leave you be :)