Gmail Mail Fetcher is on way to transfer email from gmail to GApps:
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Solutions Home Page
http://www.google.com/enterprise/marketplace/
The free program gXFER handles all combinations of email transfers involving gmail and GApps mail including gmail to GApps, GApps to GApps and other combinations. No longer listed.
gMOVE is another solution that allows you to add labels. See:
http://www.google.com/enterprise/marketplace/
A 3rd way of transferring your email is open up an IMAP connection to one of your domain accounts. Then you can drag and drop messages from one directory to the other. One forum member reports that folders and subfolders in Outlook received labels in the GApps account, e.g. correspondence/family, correspondence/family/wife, etc. Another way of saying this:
You can maintain your folders when you migrate. In the GApps webmail they will show up as labels. Sub Folders will look like: TopFolder\SubFolder\Subfolder
If you connect Outlook to the gmail imap server, the folders will look the same. In addition you will have a [Gmail] folder.