To list the software installed on your ESXi 5.0 Server via CLI:

# esxcli software vib list

I accidentally did a passthru of my boot device to a vm. This is a real gotcha because then the Host cannot modify the config.

Disclaimer – this could completely hose your system, proceed ONLY if you know what you are doing (or have nothing to lose).

So I had to do a little digging and found the following very helpful articles for ESXi 4:
http://vm-help.com/esx40i/VMDirectPath/fix_config_issues.php
http://communities.vmware.com/thread/328834

However there are a couple of additional notes that I need to add because things were a little different.

I found & mounted the following partitions in my client vm (CentOS):
/dev/sdc1 – this was /boot
/dev/sdc5 – this might be the baseline config directory, not 100% sure
/dev/sdc6 – this was the config directory
/dev/sdc8 – this was /var/db stuff

local.tgz is actually inside state.tgz

So here is what I did to recover

mount /dev/sdc6 /mnt/c6
mkdir ~/working
cd ~/working
tar xvzf /mnt/c6/state.tgz
tar xvzf local.tgz
cd etc/vmware
grep passthru esx.conf 
vi esx.conf
   - from: /device/000:000:26.0/owner = "passthru"
   - to:   /device/000:000:26.0/owner = "vmkernel"
cd ../..
tar cvzf local.tgz etc
tar /mnt/c6/state.tgz local.tgz

After that I shutdown the VM & rebooted.

The system came back up, I had a little clean up & documentation to do, but it was recovered.

the update command:
esxcli software vib install --maintenance-mode --depot \
  /vmfs/volumes/host-data/patch/update-from-esxi5.0-5.0_update01.zip


dealing with maintenance mode from the command line:

vim-cmd /hostsvc/maintenance_mode_enter
vim-cmd /hostsvc/maintenance_mode_exit
vim-cmd /hostsvc/hostsummary | grep inMaintenanceMode