SE cards - except the 5900SE - have 64bit memory instead of having 128bit memory.
The memory bandwidth is cut in half, the performance is decreased by 40-50%. 64bit DDR memory was only good on the GF2MX cards, as a rival solution of 128bit SDR. SE cards also tend to have lower memory/core speeds, so they significantly slower than the standard non-se cards.
64bit memory makes a 9600SE or 5600XT a lot slower, even slower than some much older cars like the GeForce3.
The SE/XT designation is truly confusing, everyone uses SE to show that the card is a slower version, but nVidia uses ATI's XT designation instead of the SE sometimes. 5600XT cards have 64bit memory, 5900XT cards are, however, full 5900s running at lower core/memory speeds. They have 256bit memory as well, they're still high-end cards. 5900SE=5900XT.
ATI uses the XT designation on its 9600XT and 9800XT cards to show that they are faster than their normal/pro models.
A brief summary:
ATI: SE (slowest) - normal - pro - XT (fastest)
nVidia: SE/XT (slowest) - normal - ultra (fastest)