ESX(i) is able to use different methods for virtualizing the CPU and associated MMU (memory management unit) instruction sets. You can configure that for a VM in its Advanced Options / CPU/MMU virtualization:
|CPU/MMU virtualization settings|
Choosing the third option will enable these hardware functions for the CPU instruction set virtualization (if available), but will remain using software virtualization for MMU instructions.
The fourth option will enable hardware virtualization for both types of instructions if available.
It depends on the CPU generation whether none, only the first or both hardware virtualization options are available. Since quite a few years Intel's and AMD's processors support CPU as well as MMU virtualization.
The default in the above dialog is "Automatic". This means that ESX(i) will choose what it considers to be the best option for the type of operating system that you have selected for the VM.
With Windows 2003 this is the "Software" mode. The reason for this is that Windows 2003 with SP1 in fact performs better with software emulation than with hardware virtualization. However, this changed with code changes introduced by Microsoft with SP2. Windows 2003 with SP2 performs better with hardware virtualization in almost any case.
Today, most Windows 2003 servers should have been updated with SP2. So, to ensure best performance you should go and change the virtualization mode of these VMs to one of the hardware-assisted ones.
For more details see the KB-article mentioned above.