Actually please don't use PDF, the Kindle can't read that format without the user sending the file to Amazon for conversion to mobi, and you can't convert PDF using Calibre without the story getting messed up. Honestly, your best bet is HTML or RTF because those are easier to convert to format of choice, it basically gives the users more options on how to get the stories onto their e-ink device. PDF is very limiting because it doesn't reflow well and only the Sony PRS line of e-ink devices support PDF (and not well at that either) Unless you know how to create a PDF that's formatted for a 6 inch screen...the story won't look good when it's moved onto the device. And yeah Kindle owners won't be able to take advantage of the correctly formatted PDF anyways.

but it would be awesome for the Tardis Big Bang stories to be in a single file.

As someone that formats a TON of stories, I highly recommend HTML or RTF (which can be added to the Sony PRS line of readers without problems but you'd have to make sure the Author and Title were correctly entered into the property fields...) I run the Ebook Library and I'm willing to help if you'd like for getting stories converted to html, rtf, or even mobi and LRF.

If you do want to make the stories ebook friendly it may just be best to actually provide a ebook ready format. Mobipocket is the format Kindle uses and LRF is the format the Sony PRS e-ink devices use. Sadly neither device can read the other devices preferred format.