As leelai said, you'll probably have to convert them to PDF or another format first.
PDF Converter will let you convert the body of your email to a PDF. You tap-hold, select all, then copy. Open PDF Converter and choose clipboard.
Once you have a PDF you can use any number of PDF annotation apps. I like PDF Expert or GoodReader, depending on what I'm doing.
There are a number of similar apps that do more or less the same thing. These are just my choices.
If the header of the email is important, I can still do it, though it requires an extra step. First I forward the email to Evernote. Then, like before, I select and copy the parts I want and go to PDF Converter to make the PDF.
If you only need the visible portion of the email displayed and some simple tools to mark it up with, you might want to consider taking a screenshot and then using Skitch. The result is a .png or jpg, depending on how it's uploaded. That's a free solution. Lots of people here use it to create quick how-to's or illustrate a point.
