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.