Higher fuel injection and boost pressures, coupled with DOHC design. But even older diesels could be tuned to make more power than stock. You'd have more smoke if you overfueled, unless you added more air. Up to a point you could easily extract 20-40 more hp and quite a bit more torque. After that, it got expensive with bigger pumps, injector nozzles, hybrid turbos, exhaust upgrades, etc.
FWIW, my GLK Bluetec is a 2.1L 4-pot and cranks out 201hp and 369 lbs-ft torque. It can (and has) made more while tuned, but it's back to stock now.
My previous X3 diesel 2.0L 4-pot made 180hp in stock form, but was easily tuned to 250hp and 450 lbs-ft torque. It was quite the unsuspecting monster. Alas, I needed a bigger vehicle and went with a new RAM 1500 diesel with the 3.0L DOHC making 265hp. The time will come for its tune as well, I have other priorities at the moment...