Just wanted to mention that the #41 SA Clone does NOT have the same body as the Clone Wars SA Clone Trooper. They may share the same legs, but that is it. The #41 Clone has a brand-new Torso, Belt, neck ball, and at least 1 arm is new.
Like Scott said, #41 Clone is much closer to #6 Clone in terms of Sculpt than to the Clone Wars SA Clone. And, the #41 Clone almost seems "taller" than the other Ep3 clones do. I think the ball-joint on #41's waist makes him slightly taller than the other Ep3 Clones because they just have the 1-peice torso.
However, the Target Clone Trooper is the Clone Wars SA body with an Ep3 Head. When you compare the Target Clone Trooper to the CW version, they are almost a perfect match. Same torso, arms, belt, etc. The only difference I can see if the head sculpt.
While playing around with my Clones last night, I have to admit that the Target one (based on the Clone Wars SA version) is much more "fun" than the #41 version. He has no goofy antenna sticking out of his back, his joints are a bit tighter, and his belt is much less "big" - if you look at Scott's picture you will see what I mean, #41 has a big belt!
I rank them like this:
#33 Clone Commander - wow!
Target Clone - great neutral sculpt
#06 Clone Trooper - non-intrusive action feature = OK with me
#38 AT-TE Gunner - his elbow joints are the only thing I don't like
#41 Clone Trooper - his antenna really bugs me for some reason
#34 Clone Pilot - somebody had to be last...
Just my $0.02 on the Clones...