Few weeks late and many dollars short, but...
One big trap I accidentally fell into was leaving emails in the inbox that actually had non-email NAs. For instance, an email from the library telling me that one of the books I'm using for my dissertation has been recalled needs to go on my @Home list so that I remember to put the book in my bag before I wind up with a hefty fine.
Sometimes I would look at my @Action tag in my gMail and despair that so many of those actions weren't getting done...then I realized it was because their real context had absolutely nothing to do with email.
So I would say, emails whose replies will take more than 2 minutes? Leave those in your email system. Emails that are actually triggers for tasks that need to take place outside your email? Get those into the rest of your system.
YMMV, of course...such is the nature of creating your system.
ETA: I should add that the reason I say "inbox" is because I use Priority Inbox in gMail. "Important and Unread" and "Unread" are my buckets for processing, but then I can have an "@Action" inbox where I store only the read and processed Action emails. Each section is collapsible so I'm only viewing one at a time, and I love love love it.
Collect. Process. Organize. Review. Do. That really is all there is to it.