I have always found it confusing that my Google Apps account users cannot use all of Google's services. My Blogger account, for example, uses a regular Google account, even though it was created with my Google Apps e-mail address. After looking through dozens of threads in Google Groups, I think I figured out the differences between Google Apps (Hosted) accounts and Google Accounts.
Google Apps accounts, also known as Hosted accounts, are a completely separate type of accounts. They can have their own domain name, but only a limited of applications are included. Among those are Google Docs, Google Talk, Google Sites, Google Pages, a special version of iGoogle (start page), and a special version of GMail.
Google account have access to all the different applications provided by Google. However, they cannot use their own domain name and do not have collaboration tools.
Hosted accounts (Google Apps accounts) are not the same as Google accounts. However, a Google Apps user can sign up for a Google account using this Google Apps e-mail address. This would give the user a feeling of having the same account all across, even if the accounts are not sharing data.
I hope this helps clear a few things for Google Apps users out there!