Google is now trying to clean that up and i've had the pleasure of experiencing that. Its not pretty. What they essentially do is if you have a google apps email address that conflicts with a normal google email address they rename the normal google email address to something different, like "foo%domain.com@gtempaccount.com" then for a few of their products they automatically migrate the data over for you. For the rest they have help available for how you can do it manually. Not all of of these solutions work and each is different.
Google also doesn't indicate the odd states you can get in along the way. After the initial migration things were OK for me, not everything migrated, but from the web the things that did were accessible. But all my authentication failed on my iPhone, OSX Apps etc. The applications could no longer authenticate with my Google account because the accounts were in a messed up state. Google provided no help on this and after much searching I found a thread that told me what had to be done. The net is that I had to change that temp email address they had assigned to something else. Once I did that all my apps on the iphone and desktop started authenticating and worked fine. Again I had no indication from Google that I needed to do that, things just broke.
After that I spent an hour iterating through the list of google services and making sure I had migrated their data. The final step is to blow away the Google account (not google apps account) but i'll wait a bit to make sure I have everything I need to do that.
Software development is difficult, predicting future messes is especially hard but for millions of people to go through this is inexcusable. Only because their products are free can they get away with this sort of thing and its part of the reason Google has not really found a way to make money beyond ads.
