I agree that it is next to impossible to protect your graveyard effectively.
Ground Seal is a cool card, but it does nothing against a Bojuka Bog-effect. It also hoses any attempt to target your own spells in there.
You could always give yourself hexproof with cards like
Leyline of Sanctity or
Orbs of Warding, but I'm not totally convinced they are worth a slot in the 99 unless graveyard hate is a huge problem in your meta. However, I'm not entirely sure that having hexproof protects you from
all forms of graveyard exiling effects.
Vedalken Orrery/
Leyline of Anticipation/
Alchemist's Refuge/
Winding Canyons could help you cast important cards from your graveyard in response to an exiling attempt.
I second the motion that your best bet is to be able to re-fill your graveyard quick enough. I'm lucky that my meta doesn't have a whole lot of graveyard hate so when I play graveyard decks, I don't feel too vulnerable.