That is a bit like asking someone with multiple children - which is their favorite...
Advantage of 2006 vs. 2003 - you can get a coupe - I have personally prefer coupes these days. Slate is a 2006 color that is rare.
There is a base performance difference straight from the factory on Gen 1 vs. Gen 2 vs. Gen 3 vs. Gen 4.
2006 is the last year that is drive by wire.
I remember when we had our 2004 and went to the local monthly VCA meeting (we were the only Gen 3) - let's just say it was a dyno day and afterwards there were many more gen 3's.
Either way be sure to call Ben Keating - site sponsor at Tomball - he will help set you up and take great care of you. He lives, breaths and races (quite well!) Vipers and is a straight shooter. There is nothing he likes better than making someone a Viper Driver. If you need his direct line let me know. I can assure you - once you own a Viper you will never be the same and everyone will wonder why you smile so much!
ViperGal