I'd also recommend to backup .kde/
And evn more important, I recommend using an archive, for example tar, to backup the Mail directory and the configs in order to avoid problems with file permission and ownership on restore.
For example when I backup my mail, which in my case reside in ~/Mail, I do it like this
Change to home directory
$ cd
create archive
$ tar cvjf mails.tar.bz2 Mail/
In case of restore
$ cd
$ tar xvjf mails.tar.bz2
Cheers,
_