After upgrading to Yosemite, Mail crashed repeatedly on my Mac. I checked several online solutions, but here is a much simpler solution that worked for me:
1. Go to System Preferences.Click on Internet Accounts.
2. Delete each of your email accounts by highlighting it and pressing the little minus bar (next to the + button) at the bottom left of the pop-up window.
3. Open Mail and be sure it’s working and not crashing. Close Mail.
4. Go back to System Preferences -> Internet Accounts. Add back each email address one by one. To do this, click on the + icon and add the information.
5. Check Mail after each new email address to be sure that Mail is still working. It will take a little time for Mail to repopulate your Inbox folders, etc., but it works.
I’ve had to do this process whenever the iPad updates its OS and the mail client quits working, so I’m glad it works for other Macs as well.
It’s a nuisance to do this, true, but it’s less onerous than trying to find folders like Mail -> Library -> Bundles or temporarily disable and then rebuild the mailboxes.
Donna M. Campbell 
thanks for that suggestion. I removed the iCloud account and then appeared to work alright, so I re-instated it. it looks as if that was enough for me.
Hi – same problem for me with Mac Mail, which was fixed by rebuilding the database for one of my email accounts (Exchange).
Select/highlight the dodgy mailbox in your Mac Mail inbox. Main menu -> Mailbox -> Rebuild
The error message I got included this line
erminating app due to uncaught exception ‘NSInternalInconsistencyException’, reason: ‘Destination store does not have a folder ID’
abort() called
terminating with uncaught exception of type NSException
Hth
Thanks for the tip on rebuilding the mailbox! I’ve had to do that with the draft folder before, too.