The M44 has just a little more power and torque and the maximums are reached at a lower engine speed.
The M42 has a quality forged crank instead of the M44's cast unit.
But the M44 has roller valve actuation which I presume would be longer lasting than the M42 setup.
Installing an M44 in an E30 would obviously involve more parts and work than dropping in another M42 from an E30. There are several features not found on the M42 (dual length intake system, knock sensors, etc) so wiring loom and computer would be needed unless aftermarket management would be used. Which would also solve the likely OBDII issues that would arrise I would imagine.
The M42 and M44 from the E36 are usually better to supercharge as they have knock sensors and a more suitable drive belt system. But as you can read in other posts (search for the Grassroots Motorsport/GRM article) there now appears to be a kit available for the E30 M42.