I just did this upgrade and it was very quick and simple. I followed the guidelines in this video from Vmware.com, do the same or go by the small guide I've written.
http://www.youtube.com/watch?v=F0wSHPSvmpk
Here are the steps you need to take
1. Make sure you obtain your new license keys from your valid account at Vmware.com, your old license will not work on 4.1.
2. Download the two patchfiles you need from Vmware.com, they are named pre-update and update and will have your from and to version in the name, ending with .zip. Upload the two patchfiles to your local VMFS store so they are ready for use.
3. Shut down all our running VMs and put your host in maintenance mode. You can do this by using the vSphere client, or you can do it on the command line as root with the command "vimsh -n -e /hostsvc/maintenance_mode_enter"
4. Run the pre-upgrade patch with "/usr/sbin/esxupdate --bundle=<name of pre-update bundle> update"
5. Run the version upgrade with "/usr/sbin/esxupdate --bundle=<name of update bundle> update"
6. When its done updating, you can either turn off maintenance mode from command line with "vimsh -n -e /hostsvc/maintenance_mode_exit" or you can just restart the host and do it from your vSphere client.
7. When your VMs are started, remember to upgrade the vmwaretools.
Thats all there is, you can do a commandline check with "vmware -v" to make sure you're on the correct version, or check it from your vShpere Client.
Good luck!
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