Nothing irritates a user more than when they receive unneccessary security warnings, and in turn nothing annoys a System Adminisrator more than an irrated user.  Such was the case recently when a customer asked for assistence with preventing Internet Explorer from prompting users when they attemped to launch executables from an internal website.  The System Administrator knew these files were safe, and his fellow employees were growing restless after continually being pestered with "Security Risk" warnings.  The solution was to enable a few helpful GPO settings that added the intranet site to the IE "Intranet Tusted Zone".

The necessary settings can be found in Computer Configuration/Policies (Windows Server 2008)/Administrative Templates/Windows Components/Internet Explorer/Internet Control Panel/Security Page.  From here specific sites can be listed in the "Site to Zone Assignment" setting, or Windows can add all Intranet Sites automatically (not as seure but easier to manage) by enabling "Intranet Sites: Include all local (intranet) sites not listed in other zones".  Also, "Intranet Sites: Include all network paths (UNCs)", and/or "Intranet Sites: Include all sites that bypass the proxy server" can be enabled.  Just make sure to read the descriptions carefully before enabling these settings, and also test beforehand if possible.

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