A speed density system uses input from the throttle position sensor, the MAP sensor (engine vacuum), air and coolant temps, and rpm to calculate how much air is entering the engine. Based on that it determines how much fuel to inject and what the timing ought to be. Mass air systems have a meter that attempts to actually measure how much air flow is entering the engine, and with temperature and pressure (BAP sensor) data, it can determine the mass of air entering. It uses that to determine how much fuel to inject.
In terms of performance, both systems are comparable; however, the mass air system will tolerate a wider range of modifications than the SD system will. The mass air system is also better at maintaining fuel economy and emissions control over a wider range of driving environments (variations in temp., elevation, etc.). I've read posts about idle quality/surge issues with both systems - they are almost always due to components in the system being defective, vacuum leaks, or because people have made changes to the system beyond the range of the system's ability to cope -- and the mass air system will cope with a wider range of changes than the SD system will. As for stock vs. stock performance, the change from SD to mass air for non-CA cars occurred from 88 to 89. There was also a camshaft change in the HO line that year that accounted for a 3-5 HP difference - the SD camshaft makes more power than the mass air cam does. I believe that difference often gets attributed to the efi systems. It's my opinion that there's virtually no difference in peak power output between the systems if everything else is equal.
Hissin said - "maf is not as precise since it flies by the seat of its pants, whereas the sd has pre-programmed maps" -- not sure I agree, although I'm not entirely certain what he meant. I would say mass air is more precise as it actually measures the amount of air entering, rather than trying to calculate it based on various sensor readings as the SD system does. Seems to me that any system that is able to more accurately respond to ambient conditions, and is better able to control emissions output is the more precise system. But it's probably just semantics.