I maintain a large number of Magento installations. I tend to find Google verification scripts littered across many production servers and many times the file is created directly on the box, failing to make it into source control, e.g.:
I'm aware of the other ways of verification including meta tags, DNS records. I would be open to any suggestions that detail how you work with site verifications in your production environments.
I'm also curious if anyone has written up a blog or found some explanation of best-practices with regard to maintaining multiple verifications over time which, though I use Google in my example, obviously apply to more than just Google.