Well...it's a matter of personal choice, actually. Some tuners like the 3S, some like the 1JZ or 2JZ, and some will swear by the 4A. It all depends on what kind of car you are building.
For sprints, I'd agree that the 2JZ is a superb engine. The combination of 6 cylinders and short stroke makes it a potential torque monster. However, the high cubic capacity also means that it is actually a little more difficult to match and tune a turbocharger...or two, as is the configuration in the stock motor. Also, when talking about cars, it's all about power to weight ratio. And the power to weight ratio potential of the 2JZ is a little lower than the 3S. For us street enthusiast, also important would be the $/hp ratio, which is rather high for this motor.
For all round performance, the 3S is preferred. Being 2L or 2.2L (stroked), it's an easier motor to prepare and to tune to high hp's. 400+ bhp is easy, 600+ bhp's is just a little more cash. It's also lighter and is capable of fitting into a variety of chasis'. You also have the option of the full 4WD gearbox, or marrying it to a 3S-FE gearbox (Camry 2L or 2.2L, year 1994-97, I think). Another nice thing is that the head was designed and made by Yamaha for race applications. When tested, the flow was virtually impossible to improve further.
If you want a quick, nippy, high torque motor without the problems of a turbocharger, then the 4A-GE or 4A-GZE would be the motor for you. Fit in more aggressive cams and adjustable cam gears (Blitz 272 degree cam shafts are still considered street driveable), a spot of porting and polishing, uprated fuel system and an aftermarket ecu...and you will have a nice, efficient 250 bhp's (from a 4A-GE...the GZE comes with a supercharger).
But, at the end of the day, this is a personal opinion. And you will find as many opinions as there are tuners out there.
As a matter of interest...
a) Toyota's Formula 4 Kart car runs on a 4A-GZE revving at 15k rpm.
b) Toyota's Supercar Supra runs on a 3S-GTE.
c) In Japan, tuners have managed to get the 3S up to 1,000 bhp.
d) In Australia, a 3S-GTE powered MR2 was brought up to 750 bhp with just off the shelf upgrades.