SQL Server 2012 comes with a new licensing model. Instead of per processor socket you will pay per core. Licenses are sold in two core packs with a minimum of four core licenses needed per physical processor (even if that processor only has two cores). The price per core is about one quarter (1/4) of the price per processor today. This means that the price for anything but quad core processor architectures will either go up, in the case of hexa core processors, or will give you less value then what you are paying for, in the case of dual core processors.
As far as how you would design your environments to keep the value without increasing the cost that means going with quad core as far as possible instead of for example hexa core. Especially if you are not sure you need that extra bit of processing power.
Although this change is explicitly announced for SQL Server and so far does not extend to BizTalk Server, the way the development of processors is and has been moving over the last couple of years it stands to reason that this may very well be (and by my guess will be) extended to other products in the future. The change is inevitable.
Therefore, today I would opt for quad core processors over hexa core if I use physical servers, in both SQL and BizTalk, to get a smooth transition to new licensing models.
Or at the very least, think twice before you go on old preferences and choose as many cores as possible just to get the most value out of the current licensing model.
Virtualization stays pretty much the same, that is, either pay for the virtual cores or for the physical cores (under the same rules as stated above).
At this point in time this is not new information. For licensing technicians this is a well known fact, but for other technicians or architects, this information might not have surfaced yet.