To update esx/esxi using a downloaded bundle on a web server, run the following command from a shell command prompt (console/ssh):
esxupdate --bundle http://web.server.name/path/to/files/update-from-esx4.1-4.1_update01.zip update
*Update*
For esxi 5, run the following command (must be an absolute path to file)
esxcli software vib install --maintenance-mode --depot /scratch/downloads/ESXi500-201207001.zip