How can I stop certain folders being replicated as part of the user profile?

Start the registry editor (regedit.exe)

Move to HKEY_CURRENT_USERSoftwareMicrosoftWindows NTCurrentVersionWinlogon

From the Edit menu select New - String value

Enter a name of ExcludeProfileDirs and press Enter

Double click the new value and set to the relevant areas, separating them by semi-colons, for example
Local SettingsApplication DataMicrosoftOutlook;Temporary Internet Files;Personal
Click OK

Close the registry editor

Start the Policy Editor (poledit.exe)

Create a new policy (or open an existing one providing it was created after SP4 installation)

Double click Default User

Expand 'Windows NT User Profiles'

Check the 'Exclude directories in roaming profile'

In the data box type the name of the directories to be excluded
Click here to view image

Click OK

Save the policy to the netlogon share of the PDC