I love this question... and I hate this question too. So many variables and potential contradictions. But here we go.
The best blower system needs to:
1) Give the greatest HP/speed gains
2) Not blow up your engine
3) Give your drive a chance to live
4) Be good value for the money
5) Be easy to install on nearly stock engines
6) Look good!
Sticking to nearly stock engines makes things more affordable and easier to install, but it eliminates purpose built, big $$$ blower engines with PSI or Quad rotor screw compressors. The contest is between Roots, Whipple and Centrifugal, using the criteria listed above.
IMHO, only the centrifugal blowers can make the big HP numbers on nearly stock engines. They have high compressor efficiency and the way the blower is mounted on the engine leaves room for a huge intercooler. This is very important because detonation is the real limit to how much HP you can make, and the coolest possible intake temperatures are needed.
Dean Nickerson gets 950 HP @ 6000 RPM from a Vortech V-4 blower and a single carb on a 498 CID engine with ported GM cast iron heads and a small solid roller cam. Before installing an Rtech supercooler he was making 850 HP. The extra 100 HP with the supercooler is partly due to cooling but also to much lower restriction to air flow. The same Rtech system on a stock HP500 will make 800 HP @ 5600 RPM. This is affordable $/hp. Dean is still using his stock Bravo drive, although I don't see how it can last much longer.
You could make 950 HP with an intercooled 14-71 on the same engine but you would need much better aftermarket heads. The better heads compensate for the lower efficiency of the roots blower and the small roots intercooler. But the heads would cost more money and the Roots system would be more likely to wreck your drive. The single Whipple has great bottom end torque but you can't make this much HP with a single Whipple, and the Quad rotor would cost more money.
As far as looks go I'm biased. I think the supercooler looks much better than the usual plumbing found on centrifugals, but I know many prefer the look of the roots blower.
That's my $.02. You can easily change my conclusion by changing the emphasis you place on each of the above variables; that's what makes the question so difficult to answer. Any time the magazines try to approach this issue, there is a lot of such debate and usually "everybody is a winner".
There's only one thing for sure...you need a blower!