I only see 2 differences is the SE can use faster RAM up to 2000 where as the P6T only goes upto 1600 and they switched to Realtek on the onboard sound looks like it might have a different Raid controller too.
Both have Realtek® ALC1200 8 -Channel High Definition Audio CODEC
Both have JMicron® JMB363 PATA and SATA controller
Both have 2000(O.C.)*/1866(O.C.)*/1800(O.C.)*/1600(O.C.)/1333/1066 Memory
I think all the newer revisions/versions (probably made in early 2010) have the higher quality capacitors (red color).
I was searching online in regards to the differences between Asus P6T and the P6T SE. I was also a little bit hesitant to purchase the P6T SE in that I may get an inferior product in terms of construction wise.
However, I am happy to say that I purchased the Asus P6T SE at my local Fry's two weeks ago and all the capacitors are red, unlike the half purple & half red in the earlier pictures (for example, NewEgg shows red & purple as do pictures of the original versions last year).
I wanted to let people know that they are indeed red, and the motherboard is working beautifully. I believe the main differences between the P6T SE and the regular P6T are that the P6T SE has lack of SLI support and removing a few other small features.