Let's talk some more email philosophy. An email client should help you quickly get through new emails, on your schedule, and turn them into whatever you need them to be once you've read them. Then it should shut up until you call it again.
Again, I'll point at Merlin Mann as my original inspiration, and if you want to hear more about the reasons behind this line of thought, go listen to his recent podcast appearances.
Further - I'm against unread counts, against new-mail sounds, against pop-up notification of new mail. I can't think of a job you could have where there's a good reason you should be interrupted by an email client for every new message. Sure, some things are important and ought to interrupt you - but there are a host of better technologies for urgent communication - IM, SMS, Phone calls, etc.
I'm for search, against filing. If you're shuffling email into folders, part of what you're doing is building an index. Computers know how to index text, and they can do it faster and more completely than you can, so stop wasting your time - especially if you're just filing it according to data that's already in the message, like sender or date. If your filing system is adding some information to each message, then a client should just let you add that info quickly and then index it for you. Not enough clients do this well.
Finally, like many people, I work at a big company that runs its own email infrastructure and won't be giving control to Google any time soon. This means that while GMail is an interesting case study and a useful option for personal email, I need to use another client for most of my email. That's why mikechecksmail is about desktop mail clients. I use a Mac, and so it's about Mac desktop mail clients. That said, I won't ignore other systems - good ideas are good ideas.