I have two copies of IE:
Version: 6.0.2900.5512 Update Versions : SP3
Version 6.0.3790.3959 Update Versions : SP2
Which one is the newer one? T_____T
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That is the newest one. Update versions usually refers to the Windows service pack.
Incase you were wondering how software versioning works with Windows/Microsoft (as you can tell if you have Visual Studio), see this answer for details.
6.00.3790.3959 is newer.
SP3 is referring to Internet Explorer 6 for Windows XP SP3
SP2 is referring to Internet Explorer 6 SP2 for Windows Server 2003 SP1 and Windows XP x64