This is an oldy, actually surprisingly old.
The "right" way to do this --- barring some better "right way" is ...
game whatever -hipnotic // FitzQuake uses "game" as the command in-engine.
gamedir whatever -hipnotic // Every other gamedir switching engine (id Software's Quakeworld, DarkPlaces, JoeQuake, etc.)
Extra params like "-hipnotic" or "-rogue" or with user made mods like "-quoth" or "-nehahra", the change can only successfully go into effect during a gamedir change since the HUD images have to be reloaded.
[p.s. It looks like DirectQ and other MH engines might already support this precise method, which isn't surprising since this is the "right" way to do it. I finally got sick of having to restart Quake to indicate the special gamedir extra of -rogue, -hipnotic or -quoth ... or -nehahra).]
Yeah, this thread is older than dirt but I didn't want to start a new one.