I purchased my 2000 GS400 a year ago. Off the top of my head, here are some things you should look at:
1. Front bumper/grill/hood is prone to rock chips, if it is really bad, have the dealer repaint/replace.
2. When driving, turn everything down and listen for excessive raddling coming from inside cabin (mostly from moonroof/glove box). Also, listen for rattling coming from steering wheel.
3. Make sure headlights does not have excessive moisture...if so, get dealer to replace.
4. When in Drive, check the RPM for low idle, which will cause the car to idle rough. (Note: The rough idle will go away if the AC is turned on, I think also if the lights are turned on.) So, turn off lights and AC and make sure car idles smoothly. This problem doesn't occur in all cars.
These are some of the minor issues I've come across either from personal experience or reading other owners' experiences. Hope this helps.
Good Luck.