Using Group Policy to list trusted internet Explorer sites

Instead you can do this from the IE branding section in group policy.  This should keep the user's already assigned sites.

User Config --> Windows Settings --> IE Maintenance --> Security --> Security Zones and Content Ratings

Click on the bullet for "Import the current security zones and settings" then click on Modify Settings.  Now you can go to Trusted Sites or whatever zone you want to add sites to.

So are you recommending using User Config --> Windows Settings --> IE Maintenance --> Security --> Security Zones and Content Ratings instead of User Configuration\Administrative Templates\Windows Components\Internet Explorer\Internet Control Panel\Security Page\Site to zone assignment list?  

I set the User Configuration\Administrative Templates\Windows Components\Internet Explorer\Internet Control Panel\Security Page\Site to zone assignment list setting back to "not configured" and then enabled the User Config --> Windows Settings --> IE Maintenance --> Security --> Security Zones and Content Ratings setting you recommended.  Each time I add a site tot he trusted zone and close the group policy, the site does not stay.  If I go back to the setting, there are no sites listed.

When you click on Security Zones and Content Ratings change the bullet uner Security Zones and Privacy to "Import the current security zones and privacy settings"

Click Modify Settings (Continue if y ou get a warning about enhanced security configuration)
Click Trusted Sites
Click the Sites button
Type the Address of the site and click Add
Click Close
Click OK then OK again.

This should keep your settings.  I just tested it from within Group Policy Management Console and it kept my settings and applied them to a test client using the above instructions.

If I uninstall IE Enhances Security Configuration from the Control Panel of the Domain Controller, I can follow these steps adding the site, and the site stays, but does not push out to the client machine.  The client is running IE6, so no enhanced security option there.

We had the same problem when trying to create a GPO to only configure intranet zone without restricting other zones. We ended up with creating a custom ADM-file with modification of the hive under
HKCU\Software\Microsoft\Windows\CurrentVersion\Internet Explorer\Domains

I would install GPMC on an XP client and configure the GPO from there.  I have never tried directly from the server so I'm not sure what the issue may be.

http://www.microsoft.com/downloads/details.aspx?FamilyId=0A6D4C24-8CBD-4B35-9272-DD3CBFC81887&displaylang=en

Sorry, I didn't specify where I was running GPMC from.  I am running it from an XP client, not directly on the server.
If I configure the site under User Config --> Windows Settings --> IE Maintenance --> Security --> Security Zones and Content Ratings, I do not see it show up on a client PC.  I only see the site enforced if I configure it here:  User Configuration\Administrative Templates\Windows Components\Internet Explorer\Internet Control Panel\Security Page\Site to zone assignment list

Using this second setting I listed I can get the site to show under the Trusted Sites zone.  What I was hoping was to be able to push sites out without removing what users may have already individually listed in their IE settings.  Doesn't look like this is possible?

Try this just to make sure it's not a GPO problem in itself.

Create a new GPO with a different name.
Set this setting and apply the GPO to a user or group of users.
Go to one of the clients and at the command prompt run gpupdate /force
Then run gpresult
look for your new policy to make sure it was applied
Have a look in IE and see if your site is in trusted sites.

No luck.
I had originally been modifying the default domain policy with this setting.
As you suggested, I created a new GPO and modified the User Config --> Windows Settings --> IE Maintenance --> Security --> Security Zones and Content Ratings setting adding 2 web addresses to the trusted sites zone.
This was done via GPMC on an XP client machine.
I ran gpupdate /force and then gpresult on a test box and the "IE Trusted Sites" GPO I created has been applied to the user settings.  Those two sites, however do not show up in IE under the trusted sites zone.

That's very strange.  I just tested this yesterday and it worked fine for me...not sure what is going on over there...I'm out of ideas...sorry :(

FYI - MS Best practices state never to modify the default domain policy with the exception of setting password policies.  The reason for this is you cannot just delete and re-create the Default Domain Policy if you mess it up.  You should create a separate GPO for each type of setting you want to change (1 for IE Branding, 1 for desktop lockdowns, 1 for security settings, etc...)