I can't comment on the 06 Corvette but I can comment on the C5 (I have a 99). I love the Corvette - it's really easy to modify, there is a ton of room in the engine bay to fit things like tools & your hands without pulling the motor. The CTS-V and GTO both have the LSx motor crammed in their engine bays. I think the Corvette will have, in the end, a larger market for after market parts too. If you plan on running the car hard and tracking it, I think the Corvette will be your better choice.
If, however, you're looking for luxury with some kick & a street sleeper then go for the CTS-V. I absolutly (dispite ALL the problems) love the CTS-V. It's a dream on long trips, the commute to work is very comfortable in it. I like the (even though it doesn't work) memory option and the heated seats as well as the Nav system. Now, my C5 doesn't have all those options and I know you can get a C6 with them (well maybe not heated seats) but if you're going to track the CTS-V you could potentially be looking at problems with the differential.
Either way you choose to go, you'll be getting one hell of a car!