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This is a big thing that holds me back on the iPhone: eMail integration.

On the desktop, I go through my inbox, and if there is an email that is part of a project or creating a new project, I clip it to the OmniFocus inbox, then move the email to an archive folder to get it out of the inbox. Then when I process the OmniFocus inbox, the email/action goes into a context.

When I get to that action, I can click on the -original message- link, the email is brought up, I hit reply, send it and BCC myself.

My response comes back into my email inbox, I clip it to OmniFocus, move the email to an archive folder, then in the OmniFocus inbox, type in the project name and a waiting for context.
(ctrl + option + command + K is set for OmniFocus clipping)
(option+command+K is the mail shortcut for 'move to again' In this case, my archive folder)

I haven't found a way to do this with the iPhone. And it's a pretty important part of my workflow.

I've fooled around with MailTags, but it's simpler for me to just clip it to omnifocus, move it to an archive folder, and use the -original message- link in the OF action or search for emails.

My workaround is:
I have a folder in my mail account called -hold for processing-
If I find an email to work on later, I move it to the -hold for processing- folder.

This allows me to clear my email Inbox to 0 on the go.

When I get back to the desktop, I have a daily action for:
process -hold for processing- to 0.
At that point the emails go into the appropriate projects.

There's hope that OmniFocus is aware of this and working on something to streamline. Although I can't think of a way to do it in iOS. Cross communication of applications is fairly prohibited.

The workaround that has been mentioned is to leave a computer always running, with mail running, that has a rule for messages with a certain subject or from or keyword that clips the email into omnifocus. Omnifocus then syncs to MobileMe or some other webdav server. Then the iphone/ipad syncs to grab the action.