No matter which one you buy, you will want to register it with Stardock's Impulse digital distribution platform so you can get all of the patches that bring you up to the current version.
If you like having physical media and game manual, then get the box and just register your serial number and get the patches for free. If you dislike having to deal with boxes and DVD's, buy it and download it directly off Impulse.
The main thing is to not buy it used because that serial number already got registered by someone else and you will not be able to patch your game.
You also may want to consider buying the "Bundle" that includes the Entrenchment expansion. You can find it on www.impulsedriven.com
Hope that helps, I don't know specifically what is in each box -- I would assume it is whatever was the current version at the time it got printed at the factory.
