I've been a folders/IMAP user for 12 years. Over the last year, I have been trying to manage my email better, and have tried many different solutions with mixed results. What I have done is this, and it seems to work really well.

I have one primary mail account I use, that other email accounts flow into. I also use my primary for personal and business, because I am my work. Using MailTags, I tag incoming emails with the "folder" name I would have put it in before. I also tag it with other things such as a project, or whatever I deem necessary at the time. Then, I have 3 IMAP folders, Personal, Business and Junk/Spam. Everythings gets tagged, either automatically or manually, and I move it manually to Personal or Business, so I maintain control of my inbox. I flag things which need my response before putting them into their destination IMAP folder. Spam/Junk is handled by a combination of server based spam filtering and mail client filtering, and this is done automatically, I typically don't have to mess with it because it works.

I have smart folders setup to show my "flagged emails" and any emails in my INBOX. These are my "action" emails or emails that need action. My inbox remains clean, I still maintain my "folder" philosophy, using one for Personal and one for Business, and I use Tags for everything else. I can then make Smart Folders based on tags, based on my need at that time. This changes all the time so do my smart folders.

MailTags is setup to update the header in cleartext, so I can use other mail applications to search for things based on my MailTags header, even if not using Mail.app w MailTags. Works with almost any webmail program. On my iPhone, while I can't "flag" an email (yet) or use any smart folders, I still have the 3 basics, my inbox, my personal and business folders. If something requires to be flagged, I will leave it in my inbox until I get back to the computer or use a webmail solution to flag it before filing it away.

I have had MailTags a long time, but have never really used it until I adopted this plan, partially recommended by Merlin in the Zero Inbox articles. Having MailTags update the IMAP server and store them in cleartext inside the header, gave me a "forward migration" plan should I choose not to use MailTags in the future.

Of course, none of this implementation would work with GMAIL, you'd have to get a real IMAP account somewhere - but would overall probably give you more flexibility than GMAIL.