A journal is asking whether we want to go with a CC BY or a CC By-NC-ND license on a paper. Which one should we go with?

CC-BY means that anyone can use it but they have to give you credit. General rule of thumb is that this is favoured by funders. CC BY-NC-ND is restrictive, not only does it not allow commercial use it doesn't even allow modification.

For more details see our page on "Guidance for on Open Access Publishing"

Should each version of my paper (e.g. preprint/final version etc) have a different DOI?

Yes. This is fine. Your paper will go through 3 versions:

1. Pre-print (the version your first submit for publication)
2. Author Accepted Manuscript (AAM) - the version after peer-review corrections
3. Version of Recod (VoR) - the version in the journal (with the publisher's type setting)

Typically, you submit to a pre-print archive before the paper is published by the journal, so your preprint will get a DOI. Once it is accepted for publication you can then update the pre-print to the Authors Accepted Manuscript (which will get a new DOI). Both versions will be available on the preprint archive, but the updated version would be the one you see when you first land on the webpage. When the paper is published the publisher’s version gets another DOI, and usually you update the preprint so the page includes a link to the published paper – both the preprinted versions are still available though. This is the ideal situation because the journal version may be behind a paywall, but the AAM is exactly the same paper, just without the formatting, and is now freely and openly available.