Hopefully this helps … http://www.microsoft.com/biztalk/howtobuy/default.mspx. BizTalk is licensed by server processor. A single copy of standard means you can put it on a box with a single CPU. If the box was dual-proc, that means two licenses.
Now with BTS 2006, "applications" is the concept, not parties. It about being able to separate out artifacts into separately managed containers that represent different trading partners, systems, etc. Each "application" can contain any number of receive locations, send ports, etc.