If you are just starting out, buy either standard or extra, and upgrade later. As for your questions...

bone animation is, as stated, the process of "lumping" vertexes together to make animation easier.

physics objects are the number of objects that can have the standard physics engine applied to. NOTE: You can write your own physics, in which case you can have unlimited physics objects. However, if you ues the default physics engine, your edition will limit you...

beam generator, i believe, is the particle engine. Particles are tiny objects that are mostly used for looks, such as fire, and explosions.

Shaders are 3d illusions that give your textures different effects. Look in the shader forum for different examples,as well as on the wiki... there are a few good screenshots there.

I/O port control... not 100% sure what thats about, but it most likely has to do with multiplayer games. I would imagine it has to do with users connecting to a host, but dont quote me on that .

So... based on that info, you may make a decision. A tip from me to you, you wont use most of these features in your first couple games, mainly shaders and physics, unless you have some expierence. (because you have to ask what they are, I will assume you dont haev much expierence) Again, extra will work for now, commercial will fill most needs, and pro is really only for those of us who are...

a) very rich
b) looking very seriously into developing commercial games

Regards

Raddaddy