Well, I'm currently using my...6th(?) FG grinder at the moment so I figured I would vote on which ones have given me the most trouble with each of them:
Hermes: Sometimes I think that without fantastic draws on your end and horrible draws on his end this guy is impossible to counter even reasonably well.
Rainbow: The sheer amount of control from this one is unreal. The only deck I've seen crush Rainbow is Voodoo but all else has major problems.
The last one was a toss up between Graviton and Dark Matter. Dark Matter has terrible amounts of Black Holes which spell ruin for most Rainbows. However, mono or duo decks can shrug off his assault most of the time, and my current timebow actually generates so much quanta that I can overcome his Black Hole spamming even with Gravity Nymphs on the field. Graviton has control and the ability to bypass defenses completely. In the end I went with Graviton.
Graviton: I haven't seen any one of my grinders even come close to creating a reaonable counter against this guy; any reasonable FG grinder uses Shields to shrug off damage, and he just blows through them like they don't exist. That on top of Explosions, growing creatures, Otys...yeah Graviton deserves that 3rd place.