The Spec offers (from what I remember) better wheels, more power, and stiffer suspension over the SE-R. Something along the lines of 180 vs. 170 bhp (though I'm sure torque numbers are probably closer). You also probably end up with a spiffy spoiler, body kit, and Spec V logo.
If I weren't so in love with the WRX and STi, I'd take the SE-R Spec V anyday.
I also like the looks of the MP3, but it's too underpowered for me. Though the Lancer is coming over soon, so let's see if that supplants the Spec V in my hierarchy of cars (sorry, it'll never beat out my baby the WRX, heh).