andreasamann.com/MacOSX/Mail_Scripts Scripts to delete duplicates and other good stuff.

Snow Leopard (10.6) has a problem where it duplicates messages.
Solution from the end of a long discussion thread:
discussions.apple.com/thread/2133249?start=375&tstart=0

Those having this problem, please use the Finder to open Home/Library/Mail and locate the file named MessageUidsAlreadyDownloaded3. Use Get Info to see when this file was last updated -- should be after the last time new messages were downloaded?

Quitting Mail and removing this file, and then relaunching Mail will result in a freshening of the file, if it has become corrupted, but will once more download everything still on the server. But hopefully for the last time.

Ernie

Another solution at OS 10.6 - Mail is showing duplicated incoming messages ! - Mac-Forums.com
Find the file called com.Apple.Mail.plist It is in your Home folder (whatever you named it)>Library>Preferences NOT PreferencePanes.

Find that file and drag it to your Desktop. Now start up your Mail program and see if it's back to normal. If it is, you can Trash that file you moved. Mail created a new one to replace it. If for some reason you think you should keep the old file (more problems than you had before) you can. Just drag it back into the Preferences folder and click YES to overwrite the one just created.

From: Dave Marra 

Mail (Mountain Lion): Search messages
support.apple.com/kb/PH11734?viewlocale=en_US

How to find Mail messages in Lion
www.macworld.com/article/1163147/how_to_find_mail_messages_in_lion.html

Feb 18, 2012 6:18 AM
I had never used Thunderbird before, there's still lots that I like better in the Apple Mail interface. But Thunderbird is light-years more flexible in managing email than is Apple Mail, largely because Thunderbird is an open platform with excellent Add-ons available. Not so for Lion Apple Mail, which is for all intents and purposes a closed platform.

Thunderbird has an add-on: http://bit.ly/tbirdimportexport available to quickly import your Apple Mail to Thunderbird.

Entourage had always been my mainstay on the Mac, and out of all the clients, I still prefer its interface and features. Yeah, it barely knows what threading is, but it's still a sweet app with an achilles heel: It's database. I was losing email to this thing, people were getting messages they weren't supposed to, and Microsoft MVP's were telling me proper maintenance included rebuilding the database at least once a week, preferably twice. That's a joke.
Source: drunkenblog.com

Thunderbird was still buggy at the end of 2005.

Eudora 6.2.3 is like a blast from the past. It doesn't seem like much has changed on the outside for the past 5 years or more. The look and feel are show stoppers for me. Plus it has ads. Thunderbird is FREE and much much nicer. (10/17/2005) MacUpdate.com