So I assume you're using Knossos?
I think both of the systems should handle everything at maximum settings at maximum available resolutions perfectly fine. So, my personal preference:
Graphics: Just enable everything you can enable, and if you like you can disable motion debris (the space trash stuff) and emissive lighting from ships (if you like dark lighting; it's the -no_emissive-light flag from earlier FSO).
Game Speed: you can opt to not disable VSync if you like, your framerate will be capped at 60 for most monitors but it will save a bit of energy and noise for you since the hardware will be less utilised.
HUD: Everything on, but the 3D radar tends to get messy with radar icons so I usually keep it off.
Gameplay: Everything on.
And that's all I guess. You can enable the FPS counter from "Dev Tool" too, if you want. as for custom flags (my lighting setup):
-ambient_factor 75 -spec_point 0.3 -spec_static 1.0 -spec_tube 0.3 -spec_exp 0.7 -bloom_intensity 35
Ambient factor for ambient (seems to do nothing up to 70), point for laser shots light, static for sun light, tube for beam light, bloom for... bloom.
The ogl_spec flag actually does nothing for some time now.