Well, I haven't read any of the Halo books but I may be able to narrow it down.
One of the most well known things about the Halos is that they ONLY wipe out organisms that have "sufficient biomass to sustain the flood" (or something like that). This would imply that all of the microorganisms and little critters either too small to fight or produce more flood would not be effected by the pulse.
I think that this is the feature that the Forerunners liked the most: they do not utterly wipe out all life as we know it. I mean, if you take a look at a timeline of earth, it took a long, long time for single-celled organisms to develop from the primordial goo (this goo contained a slew of organic chemicals, like methane, water, CO2, and oily substances that formed bubbles, inside of which organisms developed and evolved). After that, the evolution from single-cell to Doberman Pincher took less than the blink of an eye.
So, the pulse is able to discriminate based on size.
What can do this??
Well, the four basic forces in the universe are:
1) Strong force: atomic bomb go big boom
2) Weak force: beta decay...believe me, this has nothing to do with it
3) Electromagnetic force: refrigerator magnets, electric shavers
4) Gravitational force: explaning this would be insulting
Really only the EM force is the most reasonable. Gravitational is far, far too weak. Strong would destroy, well, everything that was near it. That means no Forerunner structrues (or Halos, for that matter). Or, it could be a force we don't know about yet.
And the Halos wouldn't release anything toxic, or nanobots or anything else like that, that wouldn't make sense. They would have to be much larger to store enough of it for the galaxy.
The idea that it is EM in nature could explain the shape of the Halos. If the rings contained loops of supercooled metal, they could create a strong magnetic field (shaped like a doughnut, if you will) around it.
Now, the Halos are relatively small compared to planets. And the EM force fades in strength as a square (^2).
Wiki Biot-Savart Law. But work with me here.
They could also release a powerful beam of light. Light has a spectrum of wavelenghts, right? Low energy light is radio waves. Pretty harmless.
High energy light is gamma rays. Its released by nuclear reactions, and very deadly.
Well, the Halos could release gamma rays, killing everything except bacteria, which are able to mutate and evolve to become resistant to the gamma rays. This is a theory widely accepted by scientists, and why you never hear about a nuclear holocaust being the end of life as we know it (just the end of us).
When AR mentioned the Halos aligning, this sounds like an EM phenomenon. Again, you want the doughnuts (mentioned above) to all point to one direction, our galaxy, and synchronized to fire so that they all overlap at the center of our galaxy. Otherwise, you might miss some spots here and there, or even cancel out the effects of other Halos. With the gamma ray theory, the rays would probably shoot out in flat planes (like a sheet of glass), and you would want to "cut up" the galaxy with these sheets of radiation.
Well, its getting late here, and I'm starting to ramble on. Anyone, feel free to shoot down my theories. This is all I can come up with at this hour.
Edit: Now that I think about it, the first Halo was destroyed pretty easily by MC. One of the shards from one side broke the other side after it exploded. This would mean that it would not even be able to hold itself together under such high magnetic fields. The only possibility for this theory is that it is itself not influenced by the field created. Its been such a long time since I studied E&M: is this even physically possible? For an object to create a magnetic field and not be affected by it? I don't have the time to study it any further today.