Where the list price of a Windows Server 2008 Enterprise Edition is too high which includes 25 Client Access Licenses (CALs). Windows 2008 CAL is required for each user or device that accesses or uses the server software. Remember, existing Windows 2003 CALs cannot be used with Windows 2008. Software Assurance, which includes product enhancements and a small amount of technical support, costs 25 percent of the total license fees for Windows Server and Windows Server CALs, and is charged annually.
Windows OS have a long history of security flaws, many built into IE, IIS, ActiveX, and other components. These flaws have resulted in billions of dollars in lost business due to downtime required for patching, installing, security service packs and taking other measures.
Though it is known that, in Linux Os, more manpower may require than Windows OS. There r more command line utilities than Windows and of-course it lacks of GUI features than Windows OS. As u told, this apps runs well in Windows 2003, it is recommended that, better go for Windows 2008, if the costs do not matter.
U have not mentioned here, which SP u used here, cause, the latest version is SuSE Linux Enterprise Server 11 SP1. U can use this and gain more extra facilities than 10. At least u may try 10.4