The advantage that the superchargers have is that they can make significant power at very low RPMs. I've studied the dyno results of all of the different systems a LOT! There are cases where Whipple'd cars are making 200 HP MORE than a TT car at ~3200 RPM.
At the higher RPMs - say 4000 RPM up, either the TT or the Whipple can generate whatever boost level is desired. At these RPM's the SC is detrimental in conjunction with the TT's. First, the SC is a big honkin' heat sink right on top of the engine and secondly, the SC is consuming 125+ HP at the top of the RPM range. (This is the power required to spin the SC.)
My thoughts are as follows:
1) A Whipple is an excellent cost/benefit upgrade. If you 1/4mi the car at all, the car is going to go like stink. Most on-road go-fast scenarios are also likely handled well by the Whipple.
2) A TT car is going to "feel" a lot different. The slope of the power curve is near vertical when the turbos spool up. The TT cars will have less HP a lower R's but easily more HP at the top. (Again, for the same amount of boost, the TT will have 100+ HP advantage because they do not have to spin the SC.) Some will say that the TT may be more fitting for the GT because the slight delay of full-on power gives the car a chance to hook-up, whereas the almost instant-on of the Whipple is a quick tire shreader. Of course those that are looking for the instant-on will love the Whipple.
3) An SC +TT car has the advantage of marrying both worlds. The SC will give you the low-end power and the turbos can generate all the boost you want at the 4K+ RPMs. My opinion is that in this scenario, the stock SC is going to work BETTER than the Whipple. You don't need the higher boost level capability of the Whipple, but you will have the added HP consumption of the Whipple over the stock blower.
In summary:
Whipple - One of the best price/performance mods. Proven by many examples on the road and a lot of smiling faces.
TT - A great addition to the car, albeit at a higher expense. The car will feel wickedly fast as you hit the carrier-launch part of the power band. I also think the the TT car will give you more consistent power levels on a road course, for example, whereas the large physical size of the Whipple *may* begin to adversely effect inlet temps. Also, any perceived disadvantage of the TT is eliminated because the rpm's on a track will be more consistently in the TT powerband.
Stock SC + TT - A very unique combination. The Hennesey kit looked and performed awesome! Maybe the best of both worlds.... for those who drive their cars almost exclusively on the street and/or the 1/4 mi. On the road course track, your rpms will likely always be in the sweet spot of the TT's and then the SC is just along for the ride and some increased inlet temps. A cool mod and a nice place to "store" your stock SC. (You aren't going to sell it, anyway!)
Whipple SC +TT - I wouldn't recommended. John and Jason can certainly correct me.
Also, one of the favorites at Rally 3 was the Tungsten GTX with TT AND short gears. This may be one of the best overall combinations that you can put together.
Sorry for the long post. My $.03 on the topic.