Just a tip for people who have registered Avernum 1,2, etc on the Mac OS 9 side of things:
When you get the new X-native versions of the game and run them, you will revert to an unregistered copy.
Copy the Avernum preference files from your Mac OS 9 System Folder/Preferences/ to ~/Library/Preferences/ folder in your own home directory.
The new copies should then be registered in OS X.
(Edit: If I was a more savvy searcher, I might have found out this information quicker, as it has been mentioned before. In any event, it would be really nifty if this technique was included in the upgrade documentation.)