It largely depends on the sort of driving you do - if you do lost of short journeys, buy petrol (or electric), if you mostly do long journeys, buy Diesel.
The best thing you can do to reduce the impact is simply to drive it less - The fewer miles you do, the less emissions you create, so consider using the train instead wherever possible, and walk/cycle for shorter journeys - this latter point is most important, as Diesel cars are very inefficient when cold, and so are very bad for short journeys.
Make sure the car is well maintained, particularly any emission controls such as Diesel particulate filters and echaust gas recirculation systems.
Keep the tyres in good condition and correctly inflated - a significant proportion of the particulate emissions from a car comes from tyre, road and brake wear - this Defra Report (pages 84-85) suggests that in 2009, 12.4ktonnes of PM2.5 emissions came from vehicle exhausts, and 7.8ktonnes from non-exhaust vehicle emissions - but by 2020, the exhaust emissions are predicted to fall to just 2ktonnes, while the non-exhaust emissions would increase to 8.8.
Older Diesel cars will run on vegetable oil, which doesn't really help with the point-of-use emissions, but does reduce the overall impact, as you're not using as much unsustainable fossil fuel. Similarly keeping the car going for as long as possible - it may not directly reduce the particulates in the immediate vicinity, but it's better for the overall environment than scrapping it and creating a new vehicle. This Telegraph Article, quoting from Mike Berners-Lee's book "How Bad Are Bananas? The Carbon Footprint of Nearly Everything", calculates the CO2 emissions from a new Golf to be 22t for manufacturing + 40,000 miles (the average in the UK for 5 year's worth of driving), compared with 11t for buying a 10-year-old one and driving it for another 40,000 miles - and if you make the concious effort to reduce your milage, the old one would be 5.5t for 20k miles, whereas the new one would be 19.9t - an even bigger difference.