I'd go with either Orks or Tyranids. The great thing about Orks is that, despite their hilarity, they really ARE an immense threat. I love reading fiction in which an Eldar describes Orkishness. Whereas another race might scoff at their methods, Eldar really seem to "get" the threat Orks pose to themselves and the galaxy at large. A human might cheer when he guns down an Ork, but an Eldar is observant enough to notice that the Ork died with a satisfied grin on its corpse, and realizes the ramifications of that.
It might look hilarious when an Ork's buggy explodes and leaves a smoking crater in the ground, but there are few worlds that withstand a trillion Orks igniting their buggies at once. And it's not that Orks lack the will, they lack only for buggies. The explodier, the better. Potentially, Orks are probably the greatest threat to every race in the 40K galaxy, but they're simply too fractured to run at maximum effectiveness. As it stands, at least.
Tyranids, as they've been described, probably COULD overrun the entire galaxy, given enough time. The Tyranid incursion has thus far been like the head of a spear slowly tearing into the galaxy, widening and leaving a greater gash the deeper it drives. The trick to defeating the Tyranids, ultimately, won't be to destroy them utterly. However, if enough Tyranids can be killed so that the greater extra-galactic swarm calculates that the bio-mass to be harvested is even .00001% less than the bio-mass it has to produce to consume the galaxy, then it will probably withdraw from the scene entirely. And look for another honey tree to stick its claws in, one with less bees that sting.
The Necrons, as they stand, are still a little too ambiguous to be able to gauge the full extent of their motives and numbers. The Necrons still kind of give me the feeling that they're licking their wounds. Technically, if all Necrons want is a galaxy free of life, all they have to do is wait long enough. Even if the Tyranids don't lick the plate clean, the various races are doing an excellent job of killing themselves off as is. Perhaps every world the Imperium grinds into ashes leaves a wily and very patient Necron Lord somewhere rubbing his claws together, enjoying what might be a dusty old simulacrum of satisfaction.