Drivetrain is one of the weakest links in high powered mk3 turbo Supras, particularly R154 transmission. I know next to nothing about auto trannies and as far as I remember stock A340 transmission holds close to 400whp, built A340 can take abuse of around 500 whp.
R154 start giving problems after 350-400rwhp. I will exclude here ham-fisted individuals who can destroy R154 in no time even on stock mk3. I think main reasons of why so many people complain about R154 are:
1. Age, I never heard of anybody who purchased brand new R154 from Toyota, if somebody blows his tranny he better buy another used and abused unit instead of rebuilding blown one
2. Use of "gorilla" clutches for drag racing
3. Lot of folks don't maintain there rear suspension and destroy drivetrain parts due to wheel hop
4. In opinion of many people only Red Line gear oil has to be used if you are serious about drag racing. To be exact - Heavy Duty Shockproof 75W250 oil.
5. There were many complains about output shaft thrust washer, it can get cracked, overheated, scored because of lack of oil. Well, it is splash lubricated and has to withstand high axial forces, but use of Redline shockproof oil should cure this problem. At least I never heard about thrust washer failure in gearboxes using this oil. It adheres very well to friction surfaces and withstand very high shock load. Picture of infamous thrust washer on the left taken from www.turbosupras.com
Edit: It was recently brought to my attention that HD Shockproof is not intended for manual transmissions, for more info read this
6. And last but not least - weight of the car. Make your Supra lighter and drivetrain parts have much higher chance to survive. Below are pictures of CF dust cover for R154. Some guys take weight reduction very seriously, I wish I had skills to fabricate such details

OK, below is my personal opinion of what we have to do to make R154 live. I assume your gearbox is in decent shape, no worn out bearings, synchros  or end covers. First, if you want to drag race - treat it with Red Line shockproof heavy duty oil. Next is clutch. I used RPS 6 puck sprung disc with 3200lb pressure plate. Personally I don't like it, not because of high pedal pressure or difficulties in stop-and-go traffic, but because it killed my tranny after few launches on BFG drag radials. I cracked extension housing. RPS is not slipable at all and does not require any skills to launch the car, just rev it to 5500rpm and drop the clutch. It only matter of time how soon old and tired gearbox gives up. I think in our case we have to use mildest slipable clutch disc for our power level to avoid shock loading drivetrain parts. No need to use 4-puck ceramic disc clutch for 300 whp motor, step up to more aggressive clutch only if your mild clutch is not capable. I have already ordered Horsepowerfreaks full face feramic clutch disc, it can tolerate second or two of slipping and holds up to 700 lb-ft of torque. Will use it with my RPS pressure plate, it has only 4K miles on it and wear should be minimal. Full face disc will be more smooth engaging, another advantage is better heat dissipation due to bigger surface area. Below on the left is my RPS clutch.

Another little tip - before launch pull hand brake, get the car in 1st gear and slip the clutch very lightly to remove backlash in the ring and pinion of differential. This is another precaution against shock load, drivetrain should be "tight", no slack or play.
I got rid of my stock 2-piece driveshaft long time ago and use carbon fiber DS from Titan Motorsports. It weighs 12 or 14lb (don't remember), about half of stock shaft. CF is not as rigid as steel and helps to cushion twisting shock load on differential and gearbox. CF DS has no natural frequency and does not resonate. It is far safer than steel or aluminium, if it snaps it falls into straw-like matter and just brushes underside of the car. My DS is on the picture above in the middle, on the right - picture of the same DS of Duane Stephenson from www.carbonfibrefx.com/ . He snapped it presumably because of defective U-joint. Shit happens...
Now about wheel hop. You definitely don't want it to happen when launching hard. You will feel it like a lot of tire spin and shake, ask your mate to get your launch on video and watch your rear wheels. Severe wheel hop has potential to destroy any part of your drivetrain - differential and transmission are prime candidates. It creates hammer-like shock loads on drivetrain. There can be few reasons for wheel hop. First is worn suspension parts - bushings, dampers. Lots of negative camber will not improve situation as well. It is just plain stupid to drag race with many degrees negative "JDM dorifffto" camber. For our IRS (independent rear suspension) cars the best for launch is zero, maybe even 1 or 2 degrees of positive camber. When car squats the camber changes towards negative and you will have good contact patch. Low profile tires, even sticky compound also not suitable for drag racing. Even drag radials can wheel hop, the higher and softer tire sidewall - the better. I use BFG drag radials 275/40/17 for drag racing and Yokohama AVS Sport 245/40/17 front and 265/40/17 rear for everyday driving. Wheels are Rays Engineering (Volks) TE37 17x8.5 front and 17x9.5 rear. Maybe in future I will buy set of real drag slicks on 15" Welds.
Now about weight transfer. When you launch your Supra you want maximum weight transfer to the rear tires. Few tricks that work - first is to remove your front sway bar, helps to raise your front and reduce weight as well. Second - if you have coilovers, slack the springs to remove pretension. Car squats easier in this case. Again, think about camber, with IRS it can go too far negative when rear suspension compressed, maybe you want degree or two of positive camber for drag strip. If your coilovers rebound adjustable - set rear on full soft, especially with stiff wall tires. Front better be softer for more front lift, but too soft can cause car to unload rear tires and loose traction if it dives when changing gears.
My 1989 turbo came with 3.73 clutch-pack LSD differential. Good upgrade for drag racing small turbo cars only is to switch to 4.30 differential from NA Supras. Though 1st and 2nd gears will be very short but you will get very good acceleration in 3rd and 4th gears. Also lower gears (higher numerically) provide better mechanical advantage that multiplies torque. They are good for heavy cars like mk3 Supra, additional advantage is less load on transmission and driveshaft. One downside of this upgrade is that powerful cars will run out of 4th gear by the end of 1/4 mile. Solution here is either increasing tire size or building engine with higher redline, better both, powerful cars with big turbos will only benefit from higher redline.  AFAIK in Europe NA Supras came with 3.91 differential, it will offer only marginal benefit over 3.73 and I am not sure if I can find 4.30 here if I ever need it.
Big turbo cars will go through 1/4 mile faster with numerically lower 3.73 or less gear ratio. It helps to load engine and bring turbo on boost quicker and stay in gear longer instead of rowing through gears with less boost (torque).
Good info on mk3 differential options can be found here http://www.mkiiitech.com/forums/viewtopic.php?t=40
Interesting note - there is one manufacturer in Australia, Pfitzner Performance Gearboxes who did produced set of straight cut dog engagement gears for R154 transmission. Set included billet selector forks as well. Price is (you better be seated) AUD8500. Speed costs money. If you are interested - contact them on www.ppgearbox.com.au
On the left is another very useful piece - CNC machined heavy duty bearing retainer plate from www.marlincrawler.com , part no. MC-10075. It helps to keep main shaft of transmission tight. Price is only $45

Update - December 2006

I changed my RPS 6-puck clutch disc against new full face feramic disc from Horsepowerfreaks. And f#cked it up trying to slip the clutch launching from 4700rpm at 0.7bar of boost using 2-step. Lessons for me to be learned:
1. Don't skip on new pressure plate and flywheel for your high hp motor if they are in less then perfect condition.
2. Lightweight dual mass aluminium flywheels don't work well in drag racing, heavy solid OEM flywheel dissipate heat better. Possibly heat transfer from friction inserts to flywheel material is too poor, there were many cases when clutch discs weld itself to lightweight flywheels when launching hard.
3. I should have bought 6-puck disc, they stand abuse better, and shifts are quicker.

Next summer want to buy HPF 6-puck feramic disc with new RPS 3200lb pressure plate and new OEM flywheel. Will see how it works. Also in plans 15x9" Weld wheels and M&T ET Street slicks. Tall tires are much easier on drivetrain to compare with low profile 275/45/17 drag radials.

Update - May 2010                         
                                                    
Last summer I did my motor rebuild, measured crankshaft axial play before disassembling, was OK, within TSRM limits. To my surprise after motor teardown I found thrust bearing completely trashed, guess I was very close to crankwalk.
This is what happened after so many years using stiff pressure plate. I have to admit first 2 or 3 years I had bad habit of pressing clutch pedal before starting motor. This is big no-no with stiff pressure plate, there is still no oil pressure in the system, whatever oil was between the thrust bearing and crank pad gets squeezed effectively running dry heavily loaded thrust bearing.