I don't have extremely strong positions on this, but I would have to side with simply Linux. I understand why some would like to add (or maintain, depending on your perspective) GNU/Linux. The difficulty is the prominence of stand-alone "Linux." I realize this question may be seen as one of etiquette, but I also want to think of the readers. We don't want to confuse them unduly, which is why I recommend "Linux." I would favor a note somewhere (probably in the first instance) that indicates that the term is under dispute and that some would consider "GNU/Linux" more accurate, with links to relevant Stallman/FSF information.
I do agree that we need to be consistent with the term, regardless of which one is chosen.
I would prefer using the concept "GNU/Linux" as this is technically correct.
How about a brief description in the glossary as well?
I think we can go with "GNU/Linux," but I do think we should have footnote indicating that it is sometimes simply abbreviated to "Linux" and make a similar note in the glossary.
I think that's a good way of dealing with this. Your OER handbook -- or should I say "our" OER handbook will carry the sanction of the freedom culture -- especially when the text provides an objective and NPOV.
Having the free culture network on your side will scale this project beyond your imagination!
I should note to both you and Kim that I've made the change to "GNU/Linux" where I've found just "Linux" and changed the glossary to match.
If anyone find mention of just Linux (beyond the footnote and glossary mention). Please change.