A new version of Dockstar, a utility that offers super-charged notification badges for Mail.app’s Dock icon, has been released.
Dockstar installs itself as a plugin with options in Mail’s Preferences that let you assign up to five different notification badges. You can choose different badge shapes, set the size of each badge and select the colour you want for each mailbox.
The result is a riot of notification badges, undeniably more colourful and possibly more informative:
The new version adds support for nested mailboxes and the ability to set the counter for unread, flagged, junk, or total messages:
It also offers the option to play a sound when each the count increases for each badge and comes with a screensaver and Dashboard widget.
DockStar is shareware (USD 8). A demo version is available from the developer’s web site 
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[Thanks, Tyler]
I have been needing this. I have mail route messages into folders, so when they are unread, it doesn’t show up on the Dock icon. (If this was free,) Great solution for that annoyance.
Herkamer, MailEnhancer may provide the freeware solution you are looking for.
The best thing about DockStar for me is that it allows me to turn off Mail’s dock icon notification for new mail, which is distracting, and pointless to me since it only displays new mail in the inbox (I have rules to filter most of my new messages to other mailboxes). By setting all of Dockstar’s badges to notify me of unread mail in mailboxes which never have unread mail in them, I’ve stopped any notifications appearing on the dock icon and I can go back to relying on MailUnreadMenu which notifies me discreetly about all my new mail and not just what’s in the inbox.
What I’m looking for is an app that will allow me to change the color of the mailboxes themselves within the mailbox pane of the app. So, for example, the 5 mailboxes that are the core of my GTD processing methodology, I’d love to make red or some color that makes them visually standout from all the other blue ones. Is there any way to do this?