In the process of trying to recover data in bulk from what I assumed was a failing hard drive, Windows Security kindly notified me it had found a handful of malicious items among the recovered files. I immediately nuked that secondary drive, but for a few items it reported either "Remediation Failed" or "Item removed or restored from quarantine".
I did a full scan, then an offline scan, and a full scan in safe mode with Security Scanner, all of which found nothing. I have not seen any symptoms that match the items it detected, and have read that those two concerning reports are a common artifact of manually deleting items it found.
My finger is hovering over the "nuke it from orbit" button anyway, but for now I think this an interesting question: Obviously nothing can guarantee it, but what tools, techniques, or combinations thereof that can produce a higher confidence than just running Microsoft's tools in sequence? Perhaps some combination of tools run on a Linux CD/USB?