Problems with VUM (VMware Update Manager) lead me to upgrade our ESX 4 U2 hosts to ESX 4.1 using the command line. During the upgrade, I was getting an error about a certain rpm package that would not uninstall properly (esxupdate error 15), so I've included that as part of my instructions.
To prepare for the upgrade, you need to download the ESX pre-upgrade zip file as well as the 4.1 upgrade zip file. I used WinSCP to copy them to the /tmp directory on each ESX host, then put the hosts in maintenance mode using vCenter before doing the upgrade. The whole process is pretty quick once you've downloaded and staged the zip files.
Note these instructions assume you use sudo for admin tasks, if not, leave it out.
1. install pre-relase patch: sudo esxupdate update --bundle=/tmp/pre-upgrade-from-ESX4.0-to-4.1.0-0.0.260247-release.zip
2. install upgrade: sudo esxupdate update --bundle=/tmp/upgrade-from-ESX4.0-to-4.1.0-0.0.260247-release.zip
3. remove RPM from update 2 that won't remove autmatically (the first command checks to see if it is still installed, the second removes it if it is still there): sudo rpm -q vmware-esx-apps-4.0.0-2.17.261974 sudo rpm -e vmware-esx-apps-4.0.0-2.17.261974
4. reboot sudo reboot
5. Afterwards, you can log back in and check the host version: sudo vmware -v
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