I had no problems with missing apps on FreeBSD. I use the ports-system for installing my apps and nearly everything is available.
Since PC-BSD is a full featured FreeBSD you can use the ports there either. What apps are you missing?
I am a little confused about the way programs and libs are handled. So I have the possibility to install apps inside a jail (the portsjail). So I a complete second FreeBSD installed inside the jail (using it's own libs). Then there are the PBIs which are installed in special directories (outside the normal FreeBSD-directories).
Then there is the Base-System (which is a FreeBSD-Base-System - with its own libs, and the third party apps - like KDE etc. with their own libs).
So thats confusing to me
And I don't know what apps are included in the automatic update process... Only the ones in the base-system and the PBIs or the portsjail too? Maybe there are ports that I have installed in the base-system too (such as the guest additions of VirtualBox).
You know what I mean?
I needed some time to really understand the seperation of FreeBSD-base and the third party ports in a standard FreeBSD-Installation.... But with PC-BSD its even more complicated because there are more ways to install software. (I understand the behaviour of jais, but I don't understand the automagic of PC-BSD).