Typical, it had to be complicated with me!
OK, so I had growled installed before, but I couldn't find it anywhere, so I installed it again.
It didn't work with mail (or anything for that matter, tho I didn't give it a chance - I only tested mail). All the applications were showing in the list of applications in the Growl Menu.
So, I tried what is in this post. Only trouble is in the section you mention there are two folders: Bundles (with nothing in it) and Bundles (Disabled) (which has the files you talk about in it. I added in the two lines above the 10 or so other lines and saved. Restarted mail, restarted mac. Nothing. No notification for new mails.
I then uninstalled everything again and manually removed the files it says on the Growl Website. It didn't mention to, but I also put the two 'Bundles' folders in the trash (but didn't delete) to see if Growl, when I installed it again, but add a new folder in. It didn't.
I uninstalled Growl again and put the folders back and then re-installed Growl.
None of my applications showed in the preference list.
So I closed and opened mail. Nothing. I restarted the mac. Now Omnifocus shows, but no other applications.
PS - I'm on version 10.6.8