Indeed. Email headers should contain two fields, Message-ID, and References.
Message-ID must be unique, therefore I propose (capital words are variables) :
redmine.PROJECT-NAME.issue-NUMBER.reply-REPLY-NUMBER@HOSTNAME

Any email notification can include multiple references to other notifications, for exemple, for 2nd reply to issue 49 for current redmine project :

<pre>
Message-ID: <redmine.redmine.issue-49.reply-2@redmine.org>
References: <redmine.redmine.issue-49.reply-1@redmine.org>
<redmine.redmine.issue-49.reply-0@redmine.org>
</pre>

That will give, in the MUA, a very deep unary thread. This might seem a bit inconvenient, but it is the only way I see to ensure working threading for anyone subscribing in the middle of the discussion.

I can _not_ unfortunatly put this on top of my todo list, so I put it fairly deep, but if someone want to volunteer, patches are welcome.
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I think we should use something like a hash instead of raw project identifiers.
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Something like this:

<pre>
# Generates a message id for the given object
def message_id_for(obj)
s = "redmine.%s.%s.%08d.%s" % [obj.project.identifier, obj.class.name, obj.id, obj.created_on.to_s]
hash = Digest::MD5.hexdigest(s)
host = Setting.mail_from.to_s.gsub(%r{^.*@}, '')
"<#{hash}@#{host}>"
end
</pre>

What do you think ?
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I have no particular position on using readable string or hash. Why do you think a hash is better suited ?
Also, if using a hash, you should ensure to strip-out any character in [<>@], as specified in the internet text messages RFC.
Also, for objects having multiple revisions (edited message content, edited wiki page), message-id must be uniquified for each revision. It might be needed at some point in the future.
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> Why do you think a hash is better suited ?

Fixed length and [0-9a-f] only

> Also, for objects having multiple revisions (edited message content, edited wiki page), message-id must be uniquified for each revision. It might be needed at some point in the future.

Good point.

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> Fixed length and [0-9a-f] only
Ok. This adress the fobidden chars by the way.
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+1
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+1
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Headers added in r2281 for issues and messages.
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Related messages are still not getting threaded in Microsoft Outlook 2010 and 2013. Microsoft Outlook 2010 and 2013 thread emails based on thread-topic and thread-index email headers and these headers are missing in Redmine emails.
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Gaurav Pandey wrote:
> Related messages are still not getting threaded in Microsoft Outlook 2010 and 2013. Microsoft Outlook 2010 and 2013 thread emails based on thread-topic and thread-index email headers and these headers are missing in Redmine emails.

Do you have a documentation about that ? I can dig into that issue if I have a solid spec or documentation about what to add in Redmine headers. Also, I'd prefer a new issue for that, please make a new one and assign it to me directly. This issue is pretty old and already "solved" for most use cases.
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Gaurav Pandey wrote:
> Related messages are still not getting threaded in Microsoft Outlook 2010 and 2013. Microsoft Outlook 2010 and 2013 thread emails based on thread-topic and thread-index email headers and these headers are missing in Redmine emails.

It is #17096.
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Jean-Baptiste Barth wrote:
> Do you have a documentation about that ?

See #17096#note-13.

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Thanks Toshi, I let you take care of that then :)
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These links have some information about how Outlook takes care of email threading
* http://msdn.microsoft.com/en-us/library/cc765583.aspx
* http://msdn.microsoft.com/en-us/library/cc815282.aspx
* http://msdn.microsoft.com/en-us/library/cc842470.aspx
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duplicates,Closed,603,Don't include new status for issues in email subject