This game has a grand total of 45 mark hunts, of which only 1 is mandatory towards the story.
There's been many mark hunts, but which ones were your favorite?
For me, I really loved completing the Wraith hunt. It's only #4, but it was quite tough if you attempted it right away. The Wraith loved to cast Doom, a status effect at that point in the game would be incurable, and you only had four party members.
Besides that one, I really loved Deathgaze, as you fought it on the airship. That was a fun battle.