All of the Roubaix models got a "bump" in the quality of CF used for '09. The Elite/Comp went from "6r" carbon to "7r" carbon. The tube shapes changed for '09 as well. The only thing the "Comp" buys you is a few upgraded parts, most notably an Ultegra RD, Shimano RS-10 wheels, and a Toupe Gel saddle. The Elite gives you an Avatar saddle, Mavic CXP-22 rims with Specialized hubs, and 105 components all around.

I'd probably go with the '09 Elite and attempt to bargain the price down a bit. Honestly, though, that's mostly because I think it looks better than the '08 Comp...