If you mean Windows pop ups you can stop the Alerter service. If it's IE pop
ups there are numerous 3rd party tools that can stop these, try a google
search.
Open the Services console from the Administrative Tools
folder, and double-click the Messenger service. Click
Stop, choose Disabled from the Startup Type drop-down
list, and click OK. If you later need to start the
service, you must change its startup type to either Manual
or Automatic.
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