Basically you will be restricting 3rd party applications on your BBs. This is accomplished by establishing an IT Policy. The basic step-by-step:
1 In the BlackBerry® Administration Service, on the BlackBerry solution management menu, expand Policy.
2 Click Create IT policy.
3 Type a name and description for the IT policy.
4 Click Save.
5 To configure the IT policy, perform the following actions:
a. In the IT policy information section, click the IT policy.
b. Click Edit IT policy.
c. On a tab for an IT policy group, configure values for the IT policy rules. You will want to go to the Applications policy group, and set the value to restrict 3rd Party Applications
d. Click Save all.
You'll then need to apply the IT Policy to a group and push it to all the BBs in your BES system. This is all straight out of the BES manual.
BlackBerry - Manuals and Guides for Administrators
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EDIT: This policy restricts apps installed OTA (like from the App Store or from any other OTA source) as well as through Desktop Manager.