Yeah, we've suffered big time from that in previous places i've worked. One major thing to take out of it is to never use ntp within a vm. Make the time right on your host machine, and then let the vm's trust their clock. As you've seen there is lots of recommendations about changing the clock type. In terms of progressing forward more, the vmware forums do contain a lot of useful information about it. I can have a word with some contacts who were dealing with the issues more directly, as I do think they got a good solution in the end, and I bet it bites me in the arse in the future too.
http://www.vmware.com/pdf/vmware_timekeeping.pdf
http://www.djax.co.uk/kb/linux/vmware_clock_drift.html
http://communities.vmware.com/thread/120931
Looking at the 2nd link there, I *think* I do remember the disabling of smp to have had a big impact. VMware largely recommended different clock methods, with only modest improvements.
And I i wrote this ilikejam did recommend tight ntp implementations... again within vmware and other virtual environments, when you think about it, there should never ever be any need to change the time, as it is getting the time from another machine already, not a bios clock. With fluctuations in process scheduling and all that freaky stuff that a VM is subjected to by its host compared to a good old fashioned bit of tin, if you then add in another mechanism to make the time fluctuate, that poor VM is just going to get a really bad headache.