Which I find is actually quite problematic; "make install" by default puts things into /usr/local, and I would prefer to distinguish between things I've installed and things ports have installed. (Specifically, I need to build my own mplayer, but I also need the ports version installed as some other ports depend on it).

Feel free to change the prefix passed to the packages you install by hand. /usr/local is the default used by almost all packages I am familiar with, if for example you want /opt you have to modify that yourself.