My girlfriend's 2002 Honda Civic, which has a 1.7 turbo diesel engine, runs very roughly when it is first started and generates quite a bit of black smoke. The engine sounds as if it is limping - as if it is running on only 3 out of 4 cylinders. After a few seconds it is fine and it runs beautifully after that. Seems to be most common if the car hasn't been driven for a few days.
Could it be a glow plug that needs replacing - is one cylinder not firing until the heat from its neighbours warms it up enough?