I'm assuming turbo because black smoke is a sure sign that the diesel being injected doesn't have enough air to completely burn. I'll list as many reasons for that as possible:
1) Turbocharger is not spooling as well as it should - boost pressure is too low reducing air volume present in combustion chamber. Usually due to loose/cracked vacuum lines on the actuator.
2) Turbo boost pressure sensor is faulty. Directly related to how hard the ECU tells the turbocharger to provide boost (adjusting vanes). This sensor is low on the intercooler on the battery side.
3) MAFS sensor is dirty/faulty. This may or may not trigger a separate error code and push the car into limp mode. Cleaning must ONLY be done with electrical contact cleaner as the inner wire that does the work is highly sensitive.
4) Fuel rail pressure sensor return value too low. This is how many performance chips work - they reduce the return voltage on this signal proportional to the amount of throttle being applied. More intelligently produced chips (Unichip, ChipIt) also adjust turbocharger response so that not only is more fuel added, but more air too. It would be interesting to see a graph of your fuel rail pressures vs engine rpm vs throttle vs engine load to see what's happening with the fuel pump in response to the other inputs.
5) Dirty air filter. Usually this is picked up by the ECU through a combination of engine RPM (provides volumetric flow expected), boost pressure and MAFS flow rate.
6) Faulty/erratic connection on the ECU itself. Has to be mentioned, it happened recently to another member here. Also had a member here with debris in the injector connectors.
My brain's a little numb now. The most common cause - especially given the age of your car - is the vacuum hoses on the actuator. They're thin little hoses right next to the hottest part of the engine and they're always going to suffer - and often do. It's not your turbocharger itself that's being suspected - it's the control of the turbocharger's vanes which is one by the actuator which is controlled by vacuum. Oddly enough, the vacuum pump is over on the other side of the engine near the fuel pump, so it would pay to check all the hoses all the way over to there.
Checking them is cheap, often overlooked and sometimes missed by even the most careful observer. If you can TURN the hose on the barb, replace it. It should hold tight on the connectors.
It could be as simple as that, and I for one hope it is!
