Are the Windows, Solaris, and Linux versions of ArcGIS Server functionally the same?
No. At 9.3.1, there are a number of differences in functionality between the Windows and Linux/Solaris version of ArcGIS Server. The following table lists some of the known functionality/capability differences between Windows, Linux and Solaris. Most (if not all) of these items have been publicly documented in various forms throughout the on-line support resources and software product documentation. These differences are not expected to change for 9.4.