some 10 years ago, when even the slightest hiccup could make a game running in linux slow to a crawl (not linux's fault. more like greedy games on average hardware), i ran several tests to find the best settings for performance. here's what i found:
- even a lightwheight window manager like windowmaker, fluxbox or xfce impacts negatively (specially if you're short on RAM)
- any cute widget, dockapp or systray app can take a hit. a simple opengl cpu meter, displaynig a spinning cube, running inside a 64x64 dockapp had a 10% hit on glxgears' frame rate
- daemons started from init.d scripts steal memory, and if they trigger a backgroud process, bye-bye performance. so make sure anything than trigger lots of disk I/O operations are off. specially if they run from cron
- get used to the command line. shut down GDM/KDM/XDM or any other graphical login. log on the console, quickly create an .Xsession file with nothing more than "xterm" on it. as soon as X starts with a windowless xterm, run the game from the CLI.
now, optimize BOTh PC-BSD and linux this way, THEN run a benchmark. otherwise, is the same as trying to compare a default ubuntu with openBSD on which one is more secure. or the other way on which is more usefull as a desktop. it's not right to ebnchmark different OSes by leaving the defaults just like that.