Can I use this with organic groups if each group is it's own site?

I don't quite understand. You should only have to validate a domain once and you're good. Are you using sub-domains?

I'd also like to know the answer to this, I don't have groups set up under domains, but they are set up under different folders. If an editable field could be added to the group nodes, then outputted as a verification tag on the group node, then I think that would solve this.

You'd only need to verify your domain once. If groups are sub-folders, they shouldn't require verification as well as they're still on the same domain you've verified.

Since I posted this, I did figure out that you can add sub-folder sites to your webmaster tools and give users access to these reports. It creates a maintenance issue on the domain administrator to create sites and add users. If each site owner with a sub-folder could add their own code and basically set up their own account, it would be a bit more convenient, but not completely necessary. Thanks for the response.

Cleaning issue queue for out-of-date 6.x issues. Thanks!