Gmail and the Conversation
Gmail started with a wonderful idea: People often think of emails with each other as a conversation. You have all of the emails under a certain subject header grouped together in one continuous view. For times when you're talking to just one or two people, in order, this is fantastic. If it becomes more complicated than that it's just plain bedlam.
I'm on a number of mailing lists which have huge amounts of traffic and people respond to emails as they see them. This means I essentially get a random mixture of responses all simply ordered as they arrived in my inbox or as they were sent from the other person's. Take into account how YahooGroups! will sometimes send emails out in random order and it's just impossible to sort.
Because of how hard it is to comprehend where you are inside of these conversations, it encourages people to top-post, as that leaves the most of the previous message in tact. This, in my opinion, is probably the worst thing that can be done. Gmail uses a few ingenious methods to cut the cost of top-posting when trying to read the emails, but an important caveat is that we're still punishing everybody in the world that doesn't use gmail with these ridiculously huge emails.
Threading Done Mostly Right
For most things I prefer threaded views. It scales much better than conversations. Also, I rarely interact in threads where only two or there people are speaking.
YahooGroups! actually has one of the better thread views that I've seen. Gmane uses a threaded view that's just as functional and more spartan. I tend to like the way that YahooGroups! summarizes posts, but I understand wanting to use the gmane style view for huge mailing lists.
The Last Vestiges of Failure
I like the threaded view, but what's the biggest problem with it? Thread views seem to be entirely dependent on what the other person sending the email is doing. If they have a broken mailing client that doesn't mark the new post properly, then your entire thread view is fragged.
A much worse example is when you just have people that don't know what they're doing and rather than sending a fresh email to a list, they hit reply not realizing that some people's clients care who their replying to. This results in either strange and entirely off-topic posts, or brand-new posts that are buried in a thread from six months ago.
What do I want?
In something like Thunderbird, we shouldn't have this problem. All of the information is stored inside of a local mbox, so why can't I just move emails around to associate them between threads? This would mean that at least I can reorganize when the list gets too long or pull out somebody that sent a re: Blah [was: Mrah] that gets lumped in with the original thread. Maybe I want them lumped in? Who knows, but sometimes the engine is wrong and needs help.
The other thing that would be nice is some sort of flag to bring new emails straight to the top that seem to be to dead threads. We have spam detection and scam detection. Why aren't we also detecting potentially incorrect email listing? Chances are that a new email to a thread that's a year old doesn't belong. There could easily be a tweakable metric based on email volume to help decide how quickly a thread should be considered dead. On some lists I'm on, a thread is dead after a week.