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I've got a few ideas for how the reply options can be optimized:

Per User Options.
Right now, you have one option, for everyone you follow: @replies just to you, all @replies to people you're following, and all @replies. While this is a nice feature, it'd be better if there were also per user settings. For example, let's say I'm interested in all @replies from everyone I'm following except @user1. Maybe they respond to every single tweet, even if its just for "thanks," and I don't really care about all of those. They reply with content I'm not interested in. I'd be amazing if there were options on a per-user basis for how replies should be handled.

No @replies to Protected Updates That I Don't Have Access To.
Let's say @user1 replies to @user2, and @user2 is a protected user that I do not have access to (I don't have permissions to access his/her tweets). That's just frustrating - I can't see what @user1 is responding to, which therefore makes that tweet from @user1 completely irrelevant to me - meaning I don't have a point to seeing it. I'd love to see an option in the reply settings to be able to block out replies to protected users that I lack access to.

Just thought I'd throw those two thoughts out there.

Twitter Favs + Pseudo-Stock Market Index = Twork, The twitter-members value index?

One of the things that came to mind for an application to twitter itself is creating a index value for tweets and those who use twitter. Much like the way that the stock market index is displayed, I picture twitter/tweet watch/fav values scroll by on a multiple level marquee.
"...Dantheshive +2, rsteven +12, piccolan -5..."

And it could be displayed on a plotted timeline much line how the stock market index's the ups and downs of stock. Maybe even have comparable plotted-timelines bewteen twitters. But of course, sense it will go up with choosing favorite tweets, it also would have to leave an option of negative value somehow.

I think Twitter should implement OAuth so that I don't have to give third party web sites (like netvibes or chi.mp) my twitter credentials.

This would enable me to give specific permissions to various 3rd party web sites to access certain information from my twitter account.

Is there any way we might see an AJAX-powered public timeline anytime soon? Since the election.twitter.com site is pretty similar, wouldn't it just be a matter of changing a few values (feeds to pull in)?