^^ this sums it up very nicely.
It is also important to note that the carbon soot that is produced is not as awful as it seems. People see the black smoke and smell the exhaust and assume its deadly and toxic. It does contain some nasty stuff, but not really that much more than a 90s gasoline car. Most of the stuff you can see coming from a diesel's exhaust is heavy particulates that fall to the ground and have very little impact on the atmosphere. One article in Diesel Power magazine tried to compare the amount of particulates (soot) that a typical diesel emits is about equivalent to the rubber that gets scrubbed of your tires. He was equating mass, not its environmental impact of course, but his assertion was that mile per mile, you are putting out as much mass in exhaust particulates as you scrub off your tires.
Of course, are we talking about a 50mpg TDI with 185mm rubber, or a dually with 6 massive tires and 15 mpg? Hard highway rubber, or off-road knobbies?
Either way, the article successfully pointed out the psychology that diesel haters miss; just because you can see or smell diesel exhaust doesn't make it bad, and just because you can't see gasoline exhaust doesn't make it good.
Newer diesels (08-up) use particulate filters in the exhaust to capture soot, then it uses fuel in a regeneration cycle to burn the soot off from time to time. So it doesn't really solve the issue of net carbon out the tailpipe, it just postpones it for periodic release. Urea injection is also used to reduce NOx. Some newer diesels also use throttles to reduce the amount of air being ingested during cruise and therefore reducing combustion temps and NOx.
It is also important to note that as of 2008, diesel emissions for light vehicles (including trucks) are more or less the same as gasoline. That is to say, of the measured exhaust gasses, diesel now has to fit in with gasoline emissions in many ways. There are, however, hundreds of compounds coming out of the tailpipe. Another thing to consider; emissions testing measures the ratio of gasses. It is not necessarily a good indication of how many tons of any particular gas will come out of the tailpipe for a given lifespan of the vehicle.
That was a big, long way of saying this: Diesel is not quite as clean as gasoline at the tailpipe, but that doesn't tell the whole story. Diesel fuel has a much lower vapor pressure than gasoline, so it doesn't evaporate as easily. As you will notice from many fuel pumps these days, they go to great extents to recapture the fumes from fueling because it is a very significant source of raw HC. Diesel fuel doesn't have that problem as much. Diesel fuel also has a higher BTU content than gasoline, so it theoretically takes less fuel to produce the same work. Diesel engines are also significantly higher compression which means they can typically convert more BTUs per gallon into work than a gasoline engine does.
So for me (while I have yet to see hard numbers on it) it certainly seems like a wash. The research I have seen at least doesn't suggest that I should feel guilty about driving my diesels.