A Google help center article explains that "Until recently, Google offered two primary types of accounts: A Google Accounts with access to "Gmail, Blogger, Reader, Orkut, and Web History" – that can be created with any email address. And, Google Apps Accounts issued, managed, and used with your @my-domain.com organization, that provide access to "Gmail, Calendar, Docs, Sites, Groups, and Video"."
Google recently transitioned Apps accounts to Google Accounts. For now, the integration between Google Apps accounts and Google accounts is only available to Trusted Tester, but Google promised to make it public in coming months.
However, if you use your Google Apps account to access other Google services, you'll land up with two Google Accounts, with same address – resulting in conflicting Google Account:
"For e.g., your Google Apps email address is firstname.lastname@example.org. A while back, you signed up for Blogger using this email address, which created a Google Account. Since we've moved your Google Apps account to a Google Account infrastructure to allow access to all Google products, your other Google Account will be renamed to: email@example.com. You should add the +personal extension to your email address if you'd like to sign in to your old account," explains Google.
More Info: Using multiple accounts simultaneously