As far as I know now
Minutemen:
Flaregun support
Artillery support
The castle
Unique outfit (generals uniform)
T45 paint job
Railroad:
Ballistic weave
Brotherhood of steel:
Powerarmor(including a jetpack later)
T60 paint job
Vertibird support
Institute:
Synth relay grenade
Teleport animation on fast travel
So what perks am I missing? Please add any benefits you have come across for different factions, especially any benefits that occur on completion of the main story