If I recall correctly, there's a study lying around somewhere with a Doppler test at the end of dives with and without safety stop (same ascent rates) and the ones without safety stop had a higher bubble level. Now we know that bubbles don't necessarily imply DCS, but I think that's one of the reasons to do it.
Yeah, these tests are discussed in the PADI Encyclopedia, which says Andew Pilmanis conducted them in 1975 and that "a stop at 3 metres/10 feet for as little as two minutes reduced detectable bubbles by a factor of five, and a 5-minute stop virtually eliminated any trace of measurable bubbles."
So, one might conclude that the difference between the bubble reduction gained from a 5-minute stop over a 3-minute stop is not enough to make the difference between DCS and no DCS. It also depends on ascent rate, of course. I think PADI bases their recommendation for a 3-minute stop on it being done in conjunction with a 30 fpm ascent rate from maximum depth. My understanding is that a safety stop is more beneficial than a slower ascent rate.
It's all voodoo science anyway. The only thing that seems beyond dispute is that a stop of 3-5 minutes at somewhere in the neighborhood of 15-20 feet is beneficial.