FREQUENCY: How would you recommend running Backlink Audits for a run of the mill site?

I’d say that if there’s not a problem, then monthly or even every two months is fine. If you have an issue (a manual penalty, negative links or similar) I’d say run your backlink report weekly until it’s resolved. Also if you use a tool like Moz, then you can pop in whenever and quickly check your links on a regular basis – useful if you’ve been working to earn links via content amplification.