Q. When an agent asks that a "query letter" be submitted "by e-mail," does that mean that I should send an appropriately-formatted letter on my stationery as a pdf, or should it be an actual e-mail?
A. She means you need to send it in an actual e-mail. The text should be the text of an e-mail, formatted like a letter - with text centered, italicized, etc. If you simply send a e-mail saying "Hey, my query is attached in a Word doc or PDF," then she probably won't read it.
Bottom line: Agents hate opening unsolicted attachments. Send your work as text in the e-mail itself.