Please review the IBM PVU calculation documents on IBM.com
You need to review the full-capacity and sub-capacity licensing rules.
http://www-01.ibm.com/software/lotus/passportadvantage/pvu_licensing_for_customers.html#fullsubcap
You are going to be counting physical cores and virtual cores in a VMware environment. In general, for TSM EE license you are going to count the physical cores in your VM Cluster. So if I have 2 physical servers in my VMware cluster, and they have 8 sockets each and are the new Nehalem EX with 6 cores for each socket. To license the cluster it will work out like this:
Per server PVUs = 8 (# sockets) * 6 (# cores/socket) * 120 PVUs/core = 5670 PVUs
Since I have 2 ESX servers in my cluster, the total number of PVUs will be 2 * 5670 PVUs/server or 11520 PVUs.
OK. What this means is now is that I need 11520 PVUs TSM EE to license all the VMs on the cluster. If I put on 400 VMs at 2 virtual processors each or 800 virtual cores (which is more than the 96 physical cores), I don't have to count those virtual cores. I never have to license more than the physical cores.
Now I have a situation where the virtual cores assigned is going to less than the total physical cores. I can then take advantage of the sub-capacity rules.
For example, I'm running a SQL server on the VMware cluster. I could license 11520 PVUs of TSM for Databases and cover all the VMs but here I have only allocated 4 virtual processor cores to the VM running SQL. So, in this case I would count like this:
4 cores * 120 PVUs/core = 480 PVUs. (the PVUs/core is the same as the physical server calculation)
For the SQL server VM, I will need the TSM EE license which the 11520 PVUs covers, and then the 480 PVUs of TSM for Databases. Note, that since you are taking advantage of the sub-capacity you will be subject to the PVU counting rules. You may have to use the IBM Licensing Metric Tool (ILMT) which is available at no cost.
So, when you have situation where there are more virtual cores that the physical server cores, then count physical cores. When it is the other way around and you have more physical server cores than allocated virtual cores, then you can count the virtual cores. Either way IBM gives you the benefit the lowest count.
There is no difference in cost or part numbers for a physical or a sub-capacity license.
I hope this helps clears up some of the questions around counting PVUs in a VMware environment.