Microsoft terminated all support for Windows 2000 Server last week (13 July 2009). That means you get no more bug fixes and no more security fixes.
You really should start looking at doing an upgrade for those machines, pending application support. And give your application vendors a piece of your mind if they don’t yet have an upgrade path.
MS has provided some help in the Microsoft Assessment and Planning Toolkit 5.0. It will assess Windows 2000 environments and produce reports/spreadsheets that you can use in planning for a migration to Windows Server 2008 R2 (no direct upgrade path available, even with hops between because W2008 R2 is 64-bit only).