If you want to deploy Firefox 2 with the Popup Blocker enabled; using privacy.popups.usecustom = true in the prefs.js. You may want to specify sites which are whitelisted (allowed sites).
To do this you will need to add the file hostperm.1 containing the exclusion list to the default profile. "%ProgramFiles%\Mozilla Firefox\defaults\profile"
Contents of the file look like this:
# Permission File
# This is a generated file! Do not edit.
host install 1 update.mozilla.org
host install 1 java.com
host install 1 addons.mozilla.org
host popup 1 guz.ndr.de
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