Problem definately resolved / using google apps on a few domains for different purposes - one to host a site, for another domain primary use has been the gmail implementation - nice filtering and pop3 (access it via outlook, or whatever email application you prefer) check it out youself.

Revision - this problem may be resolved :)  as of 12/20? according to a blog post I found / and on domains I'm expirmenting with also I've seen improvement.

 

here is what I knew before:

I put  together these few links

essentially if you have a site on google apps and have pages that link to it with its domain name alone ... a search engine following that will run into a robots.txt file that restricts everything. 

Problem with google hosting for your domain and robots.txt

http://groups.google.com/group/hosted-misc/browse_thread/thread/993f26e2fc83f112/1f4ae868258e1ef8

robots.txt on google apps for your domain will be set to exclude all - on the domain only way around is to use domainnamehere.com-a.googlepages.com plus everythign that links in seems to require that too
more info on the google hosting robots.txt exclusion issue

http://groups.google.com/group/hosted-misc/browse_thread/thread/2a00e011f870f0fd/0857457d9c9957d4?lnk=raot

same robots.txt problem no search spiders allowed under your domain so what is the point of doing this with google?
which is totally NOT what it says here

http://www.google.com/support/a/bin/answer.py?answer=45686&topic=9204

is it going to work?  I'd love to see google apps hosting work.