If you have the funds do the MKIV or LS400 upgrade. The LS400 is a slightly better option since it costs less, and weigh less to boot!
Personally I went with the MKIV TT brakes front and back and still believe it was the best upgrade to date. The Supra brakes BOLT on, this is a very easy upgrade. The only 'mod' needed was to cut the stock dust shield lip off to accomidate the larger rotors.
old:
dust shield mod:
new:
I went with Hawk HPS pads w/ Dixcel slotted rotors with anti corrosion (they never rust!)
Believe be this cars brakes are amazing and do not fade quickly. The other major part of a good braking system are TIRES. Do not cheap out on chinese rubber my friends. Quality tires mean shorter stopping distances.
For wheel requirements, you will need atleast a 17" rim with +35 offset minimum. Anything smaller the brakes will rub (not good!!).