It looks like Webmaster Tools might be the next service to get added to Google Apps. This would obviously make perfect sense as it would allow site owners hosting their site with Google Apps to use all the tools without any need to add their domain manually or verify it (since Google knows they already own it).

I almost forgot... here's the hint:

www.google.com/a/google.com/Lo ...

Ooh
a much awaited thing
Thanks Tony

& still waiting
not working for me, but seems like they will throw open it soon