I've done a migration recently from a Mac Mini Server to a Mac Pro. I thought that migration the server by portion (like you) would be the most normal way, but turns out that I actually mirrored the entire disk image and it worked great. I simply booted my Mac Mini in Disk mode (FireWire) and copied it over.
In your case, it might be easier to start that way and remove the unwanted apps. At least, you'll be sure to have all your settings right away.
If you don't do that and start with a clean install, you'll need at least to migrate over your OD user using the Server Admin OD. Then, you'll need to "ditto" your mail, iCal and Address Book data over. The 10.6 Admin Guides, available on the Apple support website, are very detailed on the backup procedures.