The Mail app does not have this feature. The most you can do is flag the email.
Other email apps may be able to do this. I'm not overly familiar with the feature set of third party email apps. The new Mailbox app is designed to handle your email like a task list; but I believe it is still just an iPhone app. That means it would probably work on the iPad, but look terrible.
If you have an Evernote account, you can forward emails to your Evernote email address, where you can organize, tag, and add comments. It would involve a few extra steps, but there are other benefits to using Evernote. Check out this thread to get an idea on whether it might work for you.
http://www.ipadforums.net/ipad-apps/105051-evernote-how-do-you-use-tips-tricks.html
MS Outlook is a full featured organizer/calendar/task/email client. You're probably not going to find an app on the iPad that will do everything it will; though you might find one that does enough of those things to be good enough.
Good luck.
