nvidia runs their stream processors at higher clock rates then ATI (and the GPU core). that's how an Nvidia card with 64 processors (9600GT) can keep up/outperform an ATI with 320 (3870). regardless, you can't use specs to compare ATI and Nvidia, or even different series like ATI 3xxx series to ATI 5xxx series cards. Architecture changes with each series and ATI and Nvidia build their cards in different ways. Your best bet is to simply compare third party benchmarks.
All GPUS us parallel processing. It tends to be a difference in clock speed and volumn of parallel processing. Its like AMD and Intel, CPUs run a different speeds but a slower clocked I7 can beat a faster clocked Phenom II