Well this is not strictly an InDesign issue, but I'm counting on the aggregated knowledge and experience of all you typesetters here.
So, what would be the best way of storing manuscripts? Text files, perhaps? What about formatting; markup language? Does anyone know how publishers archive them?
My money's on plain text files with markup, in unicode.
What have you got against packaging the .indd files and storing on CD or removeable drive?
Just to be safe, I might do most of the above. Definitely what Peter said, but I'd also include a PDF (at the least, to compare with the ID file in the event you open the file in a much later version that causes it to look differently), and if you wanted to (or if it was practical to) export the text as a text document. That might come in handy if you needed to rebuild the file for some reason. You could also probably extract the text from the PDF, but I'm not sure whether you would have to recombine paragraphs together the way you might in (for example ) Illustrator (which isn't intended to be an all-purpose PDF editor, by the way).