For me Dark Matter is the hardest (i won him only 3-4 times), because it is a pain to meet him with any kind of rainbow deck. When it is possible to design rainbows that work considerably ok agains any other god (using Shards and protected pulvs against Octane; Aflatoxin-Bone Wall, fire shields or thorn shields against Divine Glory; steals, PA-s and pulv against Rainbow etc), then Dark Matter nullifies all that. Fractal-Hope deck is definitely better against Dark Matter, but i am not sure if it has bigger overall winning percentage against gods than my old rainbow. It seems that it doesn't have that.
And the second place goes to Rainbow, no doubt about that.