What can I do if my paper doesn't fit any arXiv category? I have a paper (A) that has been submitted to a journal, but is as yet unreviewed, and another paper (B) that cites A. 
(The citation is necessary because A includes details of the preparation of a dataset that is used in B. The preparation is not central to B, but it is relevant.)
I am about to submit B to another journal for review. I think it would be useful to have a preprint of A available (and cited in B) in case the reviewers of B want to see it. Posting a pre-print of A on ArXiv seems to be the ideal solution.
BUT, the paper does not fit any of the subject categories on ArXiv. It is in teh area of renewable energy engineering, while ArXiv is largely confined to Physics, Maths, Computer Science. 

Should I submit the paper using a subject category that is only incidentally relevant (Physics and Society for instance, or Systems and Control), or is there an alternative pre-print archive with a borader range of categories?
The archive engrXiv is dedicated to engineering. Wikipedia has a list of preprint servers where you might find other possibilities, but the engrXiv is the only one dedicated to engineering, as far as I can see.

There are other solutions to publish preprints as well: your institutional repository or generic archives such as figshare or Zenodo. Both accept articles and will provide a DOI.