Having a mail thread, I'm only able to save the last mail to Evernote, using Evernote for GMail.
I find this quite annoying making the otherwise great add-in less usefull to me as I have to forward some mails to Evernote.
I 'm aware I can turn 'Conversation view' of and thus only see one mail at the time, but conversation mode is more important to me than Evernote for GMail, so I do not consider that a viable solution.
One way of handling this is to save all mails in thread or open/unfolded mails.
Henrik Molke Rediin Happy Evernote user since 2010