Upgrading ESX Server involved upgrading the related applications in the VMware Infrastructure Suite at the same time. Single VMware ESX Server upgrades minus VMware Infrastructure Suite applications require users to upgrade the ESX Server OS to 3.5, followed by a VMware Infrastructure client to version 2.5 upgrade.
However, most of us don't have such a simple configuration. Real VMware ESX Server production environments may consist of any number of ESX Servers, a VMware VirtualCenter Server, a VirtualCenter database, VMware License Server, VMware Consolidated Backup (VCB), VMware Tools in the Guest VMs, and the VI Clients.
Though upgrading a single ESX Server from 3.x to 3.5 is relatively straightforward, having so many different pieces across the entire VMware Infrastructure Suite installation adds complexity to upgrades. For that reason, the pitfalls I list out below have to do with not only upgrading VMware ESX Server but also the entire VMware Infrastructure Suite. A particular problem is that some settings in the local Linux Service Console may be unexpectedly modified, so it's a good idea to test systems before upgrading
Servers that run VMware ESX are usually powerful and expensive. So developing a group of test systems comparable to the "suite" of systems working together in your VMware Infrastructure can be difficult. An excellent way of doing this is to run VMware ESX Server on a small server that marginally meets the hardware requirements while running VMware VirtualCenter in a virtual guest OS on one of your existing servers. This configuration allows you to perform a number of tests before doing the real upgrade on the production network.