I recently went through the exercise of upgrading my standalone VMware ESXi 4.1 server. The process is pretty easy.
Grab the vSphere CLI from: http://www.vmware.com/support/developer/vcli/
Grab the relevant patches. Make sure you select the correct version of ESX/ESXi. I facepalmed when I realized I was trying to update using the ESX (not ESXi) packages and nothing was happening. http://www.vmware.com/patch/download/
Move the downloaded zip file to C:\Program Files (x86)\VMware\VMware vSphere CLI\bin. In a command prompt run: C:\Program Files (x86)\VMware\VMware vSphere CLI\bin>vihostupdate.pl -server <server ip> -i –b <updatefile>.zip
Reboot and that’s it.