I just bought myself a 2006 EVO IX SE and had to deal with this same issue.
As stated above, the difference is the 6speed trans and susp...but like most people on this site, i will change the susp so thats out the window --- and the 6 speed alone wasnt worth the extra cash imho.
I opted for the car in my avatar and couldnt be happier
The SE (special edition) will get you:
- Aluminum roof (like the MR)
- HID headlights
- BBS Wheels (like the MR --- BUT better color)
- Red stiching on the seats ;)
- Front lip spoiler (subtle but nice)
- SE badging
Overall, its a nice package for a nice price. Im biased, but id suggest SE.