Here's one that's probably going to be relatively uncommon but I came across it the other day and thought it would be worth a mention here:
Issue: The Transfer Site Settings Wizard in System Center Configuration Manager 2007 SP1 fails to transfer client installation methods from one secondary site to another secondary site. The error message reported is:
(Reason:Skipping the setting because it is unique to a primary site and target site <sitecode> is secondary.)
This error comes up for all settings:
System types (Servers, Workstations, Domain controllers)
Enable client push installation to site systems
Enable client push installation to assigned resources
Client push installation accounts
Software Update Point Client Installation
Enable Software Update Point Client Installation
Cause: This is a known issue with the wizard.
Resolution: To work around this issue, after transferring all of the settings from one secondary site to another secondary site via the Transfer Site Settings Wizard, simply configure the “Client Push Installation Properties” on the site manually.
J.C. Hornbeck | Manageability Knowledge Engineer