Another interesting way to hide the Windows Authentication every time when the user trying to use ArcGIS Server services. First go through the cross domain.xml in given link below
This article explains it better than I could:
If you place cross domain.xml is your web server , it asks windows authentication everytime, this really irritates the user. Here is the solution to fix the windows authentication form to disappear when maps try access to services.
1) On the server machine, go to C:\inetpub\wwwroot.
2) Right click on your crossdomain.xml file to modify its Properties.
3) Go to Security Tab.
4) Check to see if you have Internet Guest User as one of the ‘Group or user names’. This was missing from the crossdomain.xml file.
5) Click on the Add button to add a new user. Enter \IUSR_ (e.g., vamsi\IUSR_vamsi; this is the same user that you will see is being used for anonymous access in the IIS).
6) Give it Read & Execute or Read permissions.