Wow, that was painful. If you are using gmail, you will currently loose all your tags when moving to google apps (GA). You can only guess what the migration tool will support. But here are the steps I had to take to get my mail on to GA:

• First of all set up all the filters you can think of in GA I have around 40.
• On gmail, move to settings and forwarding and POP, set the Enable POP for all mail.
• Start up your mail client and start POPing all mail (thunderbird is quite good and handles MBOX format)
• When done, create a account for an IMAP capable mail provider in the client.
• Now move all mail to the IMAP inbox, sent mail as well, GA will handle it well and sort it as conversations.
• In GA start POPing the mail from the mail provider.

Sit back with a good book 8500 mails took about 48h, I did some checkup and sorting underway, added a few extra filters. The 8500 mails translated to about 3600 conversations.What I wish for in GA now is better filter handling, it’s too limited. If it's not limited i am missing something and it should be easier to handle. Also, port the java application to handle GA on your phone, love the gmail version. But then again, blackberry may have bought exclusives on GA...