Some users would want / need specific applications like skype or dropbox. But some others wants a system entirely free of non-free software
So now the installer makes this easy into the "non-free" topic:
This option has been added as the last "custom options" on the installer 
What about virtualbox? seems like it is opensource if im not wrong? 
Depends which version you are installing. The "free/libre" version has less extras than the Oracle one with some proprietary stuff, like USB3......same goes for Java.
A dangerous path to proceed on if you want to fully implement it.
Tread wary for there be dragons !
virtualbox is just included by default, and it comes from the debian repos, the "contrib" specifically, which if im not wrong means that these packages can have others (dependencies) from non-free
but the non-free one is the addons-cd, which is not needed and not installed, so i think that is just fine
I was asking to know if virtualbox should be included in this non-free list, but looks to be fine
