For many users, one of the most confusing aspects of a Google Apps implementation is the discontinuity between a Google Apps account and a Google Account. Currently some Google services are available only via a Google Account login which is different from a Google Apps login. Examples of such services include Google's webmaster tools, Picassa, and iGoogle.
To minimize confusion, I recommend that Google Apps users establish a Google Account with the same userId and password as their Google Apps account. This works, however, better integration of Google services with a firm's Google Apps infrastructure is clearly needed.
Based on a 5/6/2010 blog post from Google (http://googleenterprise.blogspot.com/2010/05/more-google-applications-coming-for.html) it appears that this issue will be resolved by the Fall of 2010 with access to early adopters in the Summer of 2010.
This is a welcome change and plugs one of the significant holes that I've found in the implementation of Google Apps.