Matt,
You'll have to keep in mind that I'm not a chemist, just an electronics engineer who happens to be an old car enthusiast, so my knowledge of the chemistry behind the formulation of fuel is rather limited. Anyway, I'll do my best!
It's not that the lower octane fuel reduces emissions in itself, just that the increasingly strict emissions laws and gas-mileage requirements of the EPA (Environmental Protection Agency) resulted in the compression ratios of engines coming down from the average they'd been at during the "muscle car" era of the late 1960s/very early 1970s.
The compression ratio of the engine is one of the primary factors which determines the octane rating of the fuel needed. The compression stroke just prior to the spark raises the temperature of the fuel mixture in the cylinder. If the fuel is too volatile, this can result in pre-detonation, the mixture actually igniting before the spark from the plug.
Pre-detonation gives rise to a metallic knocking, or pinging sound under heavy acceleration (or in severe cases, under almost any acceleration). It reduces the power available, and can actually result in increased emissions due to the fact the the whole of the mixture is not properly burned. In the long term, it can also result in engine damage.
Gasoline with a higher octane rating is less volatile, and thus can be used at higher compression ratios which would cause pre-detonation with a lower octane fuel.
The reason that higher octane gas is traditionally associated with high-performance engines is not because the fuel itself contains any more energy. It's because the more powerful engines use a higher compression ratio to extract more power from the fuel, and it's that higher ratio which necessitates the use of "super" or "premium" gasoline.
One of the main reasons for adding lead (most often tetra-ethyl lead) to gasoline since the 1920s was that it raised the octane rating, preventing knocking. As lead has been phased out, other additives have taken over.
There are many other factors which have an effect on fuel volatility though, including ambient temperature, altitude (which determines density and atmospheric pressure), etc. Many people don't realize that the oil companies actually alter the formulation slightly between summer and winter, and between high and low altitude markets to account for this.
One other point I should have mentioned is that the octane rating shown on U.S. pumps is calculated differently to that shown in the U.K., so the difference is not quite as great as you might think from looking at the numbers.
Britain uses the Research Octane Number, which -- if I recall correctly -- is virtually a high-end octane rating based on a static measurement. The U.S. rating uses an average of the research octane and a "motor" octane rating, which is calculated on a much more dynamic basis to account for varying conditions.
The result is a 4 or 5 point difference, thus the basic 95 octane gas sold in Britain is roughly equivalent to 90 or 91 octane under the American system of measurement.
In both countries, the maximum rating now commonly available at the pumps is lower than in the past, so old cars with high-compression engines often need to run with an extra additive which boosts the octane rating (and which acts as a replacement for lead, which was also used as a lubricant).
Any fellow Brits remember the days when you could buy 2-star, 3-star, 4-star, and at one time even 5-star petrol here?