I have carried out fresh installs of Domino 9 as well as upgrades from Domino 8.5.3 FP3 to Domino 9 on Windows 2003 and didn't experience any issues. If you plan to use the newly implemented IHS features (which is only available in the Domino install for Windows), instead of the "native" HTTP stack which comes with Domino, you have to be aware to select this option during your install (it is not installed by default).