I'm near the end of my ESX 3.0.1 migration. I had a few VMs that encountered errors when I tried to upgrade VMTools (They were unable to uninstall the older version). Mounting the older version iso when prompted didn't work.
FYI - After a lot of testing (love the snapshot feature), here's what worked for me
Log on as local admin
Click on the VMTools icon in the System Tray to find out what Build version you are running (under the About tab). Make a note of it. If the icon isn't there, you can run VMwareTray.exe from C:\Program Files\VMware\VMware Tools\
Stop VMware Tools Service
In Task Manager, end the two processes, VMwareUser.exe and VMwareTray.exe
Delete C:\ProgramFiles\VMware and all its contents
In Regedit, delete HKEY_LOCAL_MACHINE\SOFTWARE\VMware, Inc.
Mount the iso that contains the version that is currently installed or run the msi.