Tigerfish has covered it. The only problems I have had with my Mk2 sport is the front discs, one warped, then the new set bought, had one warped (buy from a rep dealer) and the second set seem fine. Had the sticky caliper pins and one seized caliper (sticky pins equals clunking when coming to a stop and possible wheel wobble).
As for the ball joints/wishbones, it is the high milers that will suffer (115,000 miles plus) though this is not gospel.
Apart from this, great engines, great gearboxes, lovely well made interiors, sweet ride. There are examples going on eBay with 200,000 miles plus. Buying one with the faults mentioned ain't so bad, once it is fixed you're away. Just identify the fault and drop the price offered accordingly. It is also reassuring to get one with full Lexus history, the service guy's are very thorough.
The stereo display is a problem, had mine fixed, now it is back again!
Sport = stiffer ride, nicer looks and a bit more kit (big alloys, spoiler, etc.) SE = comfy ride and most likely the Nav.
Do it, you wont regret it, just buy wisely as your post suggests you will.