To those who say that people are underestimating the Flood, yes they are correct. With the current knowledge of both parties, it's pretty clear that the Geth would lose, simply because of numbers if not intelligence, tactics, or weaponry.
The problem I find with this is that the Flood, and the Halo universe, have had a lot more material released on them. Halo has had 4 games with another planned and five novels, whereas Mass Effect spans 1 game with another in production and two novels.
So right now, the Flood win. But I wouldn't discount anything from the Mass Effect universe yet, because we haven't seen it all.