Might be a strange question but...
I run a google apps account for my own domain for myself and family members for email, calendar and contacts. Email firstname.lastname@example.org
I have found that when it comes to using other useful google services such as iGoogle, Google Reader, etc that it requires you to log in using your Google Account. A google apps account however is not a google account and then involves you signing up for a google account with your google apps email address.
This means that I now have an google account for email@example.com which now has an empty calendar, contacts, etc. This becomes confusing when different google services keep you logged in next time you visit a page only to realise that when you go to calendar or contacts from the menu up top they are empty as you are signed in with your identical G-account email address rather than G-apps email address.
This may not seem like a big issue but I always run into problems when things say they support synching to google calendar yet don't end up working for google apps calendar even though to a user they are effectively the same thing. I'll enter my details and it will sync to my Google Account calendar rather than my Google Apps calendar.
Am I going about this the wrong way or is there no way to make your google apps account also your google account? It seems they are very separate yet should be integrated.