How do I stop email messages from going into Junk Mail

We are running Exchange 2003 server with Microsoft Office 2007 clients. We have some web applications that send reminder email messages automatically to users and now the messages are showing up in users junk mail. This is a recent development, apparently having to do with the Outlook junkmail filters being updated recently. We know we can ask the user to add the sender to their safe list, but because we have over 800 users, we want to fix it on the server side. Any ideas?
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I have Understood that Application generated emails are delivered to Junk Email folder instead of Inbox
You need to define  the IMF Configuration at Global level
Gateway Blocking Configuration - Block messages with an SCL rating greater than or equal to: 8
When blocking messages:  Reject
Store Junk E-Mail Configuration
Set the threshold for moving UCE toa user's Junk E-mail Folder
Move Messages with an SCL rating greater than or equal to: 8
By Default If any email received by Store with SCL Rating of 8, it will move to Junk Email Folder
Disable junk e-mail filter in outlook.
Below is a GP to achieve the same
In Group Policy, load the Outlook 2007 template (Outlk12.adm):

Under User Configuration\Administrative Templates\Microsoft Office Outlook 2003\Tools | Options\Preferences, click Junk Mail.
Double-click Junk E-mail protection level.
Click the Enabled radio button to enable configuring the policy.
In the Select level drop-down list, select a protection level to enforce.
Click OK.
Set other policies, such as specifying to permanently delete junk e-mail messages.

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kjroxbyAuthor Commented:
I had the junk mail filter SCL set to 9 at the Global level. Do you think if I lower it to 8, the application generated email messages will no longer go in the junk mail folders? I'll try it, but I'm thinking it won't make a difference. Not very optomistic am I. I also have the when blocking messages setting set to no action. If I change it to reject, what will happen? As for the other comment, I really don't want to disable the junk mail folder via group policy.
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Rick FeeMessaging Engineer - Disaster Recovery EngineerCommented:
If it is common domains you can setup a GPO to add those to the safesenders.   I did this for a org that had 5000 users.   Here is the document I is setup for Outlook 2003 but you can follow and make a few adjustments for Outlook 2007.

Outlook 2007 Admin templates: 

Justin DurrantSr. Engineer - Windows Server/VirtualizationCommented:
You can configure the Junk Email settings of Outlook using a Group Policy

The options available will vary for each client and have it's own configuration. You will need to download the Administrative Template (ADM) for Office XP, 2003, and 2007 in order to configure each.
kjroxbyAuthor Commented:
Ok, I already have the Outlk12.adm template available in my Office 2007 GPO. Up until now, I have not enabled any of the junk mail settings. I will try some things out and see how the automated application email messages behave over the next few days. Thanks for your comments.
Justin DurrantSr. Engineer - Windows Server/VirtualizationCommented:
Good luck!
kjroxbyAuthor Commented:
I was unable to remotely run the script to add the junkmailimportlists registry key. Therefore, I ran it manually on my computer, exported the key created, used my NUTS software to create a group policy admin template, imported the template into my group policy, enabled the junkmailimportlists setting, Applied it to user computers and the registry key was immediately added to the computer.
kjroxbyAuthor Commented:
I think we can close this one. Thanks for all the help!
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