Another alternative to things like Mailbox is not using your email inbox as a project manager at all.

After 15 years of abusing my own inbox this way (5172 "unread" todos to go! yay!), I grabbed a copy of Things.app a few weeks ago, and then swept the last month of my inbox into Things (skipping everything that wasn't actionable). I use virtually none of the features of Things; it's just a hotkey bound to "create a todo for this email" with the nice property of linking the todo back to the original email. I've played with tagging and projects, but they're not nearly as useful as just having a list of todos with checkboxes.

I don't do "GTD" or any of that stuff, and I am not a believer in the value of "inbox zero", but I'm now a convert to the idea that your inbox is a crappy organizer.