Lightshafts should be on by default (and IIRC, they're already in trunk), check the launcher if the flag to disable them isn't on.
It isn't.
(note, I am using beta6 build with mediavps 3612 and some extra mods (sobek, etc.), the wxlauncher has the option to disable lightshafts and it's off as it should be, enable post-processing is on, etc)
e2: my command line:
C:\Media\FS\Game\Freespace 2\fs2_open_3_6_15r_Shadows&Deferred_Beta_6_INF_SSE2.exe -mod
SobekMod-Ultra,SathMod-4096,Arcadia,mediavps_3612,Rak-Ultra -missile_lighting -3dshockwave -post_process
-soft_particles -fxaa -snd_preload -fb_explosions -window -shadow_quality 2
plus the custom flag: -shadow_quality 2