freebsd and openbsd use the ports system.
you can either use
pkg_add -r pkgname
to install the binary package of the software. the -r switch pulls in all dependencies. or you can build from source.
cd /usr/ports/whatever/port
make install clean
netbsd uses pkg-src. i know nothing about pkg-src.
now theres pcbsd and desktopbsd. pcbsd uses pbi for software. BUT, being as that it is essentially freebsd, you can still use the ports system... which i recommend anyways.
i dont know anything about desktopbsd.
DesktopBSD is getting outdated and the release cycle is becoming very long, as a result of the main developer(s) diverting their interest into other areas. PC-BSD is very active, but I am not particularly impressed with it: the desktop still looks incoherent.
Pkd_add only works in the command line in all BSD variants and is still the most stable way of installing software (and pkg_delete to uninstall it). The uniform way of installing software that way carries a large and wide appeal.
You can mix ports and packages easily. Installing packages is faster (about 10 times as an educated guess), but is not always possible. Acrobat Reader for instance has no packaged installation for licensing reasons and must therefore be installed using the ports manner.
yes its easy to mix them, and its easy to get things screwed up because of that. if theres any backward compatibility issues with any ports or regression, then you may be in trouble with different versions of dependencies being installed.