I've recently run into a very annoying error when I tried to add a new domain (the one for this blog) to my existing Google Apps account.

When trying to verify the domain ownership Google threw up the following unhelpful error: "This service is not available. Google Webmaster Tools is not available for [domain]"

Webmaster Tools? Hey, I was only trying to verify domain ownership here... A quick search brought up tons of other users with similar issues, including some closed threads without solutions (thanks Google!).

After some more digging and failed attempts at resolving the issue (it was suggested that malformed DNS records could cause this) I figured that adding the Webmaster Tools to my account did the trick. Yeah whatever!

Log into your Google Apps account and go to 'Organization & users'. Next click 'Services' which is a tab next to 'Users' and somehow easy to miss.
Scroll down and enable the service 'Google Webmaster Tools'.

Now try verifying your domain again, it should succeed - at least it did for me.

Good luck.