I’ve used Google Apps for my domain, and until recently I wondered why I could have two separate Gmail accounts on the one login. I’ve read various explanations of how Google accounts worked but it wasn’t until I disconnected my Google Apps account from my Google Account that the truth sank in.
I started with a Google Apps account and gradually added Google services to it. I always assumed that I had one Google account, and that as administrator of my Google Apps domain, that I could reset the password etc easily if I was hacked. Not so, because what I actually had was two Google accounts that had the same login details and the same password.

It suddenly made sense why PicasaWeb would not tag my images using my Google Apps contacts, since these were two separate contacts lists on two separate accounts. I found Google Docs I had contributed to in my Google account, whereas most of my work documents were in my Google Apps account.
As a solution I migrated all my email and contacts to my GMail account (on the Google account). I could now tag my Picasaweb photos using my contacts in my address book. The contacts were also present in Google reader as well so I could now email articles to my friends. It made sense to have all my services in one common account but this created a problem.
If you’ve used GMail to send email from a different address to your own, some recipients see a “on behalf of” message – e.g. From: [email protected] on behalf of [email protected] I didn’t think this looked very professional but Google has a solution. Using the technique recommended by Google I set up another sending address but using the Google SMTP server with my Google Apps login details. Now (as intended) I can send email from my GMail account and it looks like it came from my Google Apps account, and as a bonus an extra copy of outgoing mail is saved in my Google Apps accounts.
I’m not sure that using my GMail account is as professional as using a Google Apps account, but to recipients of my email there is no distinguishable difference.
There is very little operational difference between Google Apps email and regular GMail apart from the fact that the contacts list for Google Apps accounts are not shared with other Google services. You can also add extra storage to a regular GMail account but this is not possible with a Google Apps account (unless you upgrade to the the premier version).
With many schools and businesses moving to Google Apps, I think it is important to be clear about the difference between the two types of account. It would be nicer to see closer integration between Google Apps and Google accounts but I can see the reasons why this has not been implemented.