Once I'd set up my Google Apps account I wanted to switch to using its reader instead of my old accounts one.

The thing that kept me with my old account however was my starred items, below is a method to switch and get your starred items as well:

First you will need to export your feeds from your old account, when you are logged in to your old reader account:

• Select Settings, then Import/Export
• Click the "Export your subscriptions as OPML file" link
• Save the file somewhere you can find it

Now we need to share the Starred items:

• Click Settings, then Folders and Tags
• Tick the checkbox for "Your starred items"
• Select "Public" from the "Change Sharing.." dropdown box
• Click the "view public page" link that appears next to "Your starred items" row
• Leave the public page open
• Log out of your old reader account

Then we need to log into the new account and first import the exported OMPL file

• Log in to your new reader account
• Select Settings, then Import/Export
• Click the "Browse" button to upload the file you saved earlier
• Now your subscriptions are imported

Now to get the starred items into your new account:

• Subscribe to the starred items feed from your old account, it's in the window that we left open earlier
• In the subscriptions panel select ensure that your old starred items feed is selected
• Cick the "all items" link in the view pane of reader
• Start starring all of the items
• Now you can unsubscribe from your old starred items feed as we don't need it anymore
• Your starred items will still be be available even though you have unsubscribed from the feed

I know it's manual, but I had cose to 1000 starred items and it only took me about 5-10 minutes to re-star them in the new account, well worth it if you truly want to have everything in your apps account.