I have had 3 instances where the car as left me stranded. One due to a tire, one due to the gas cap not being tightened correctly (yes, it can stall the vehicle), and one due to a bad battery.
All the comments with regard to the transmission/drive train are true. I've driven the 2003 GX470 and 2004 GX470 (loaner), and both have the same problem. When stopping, the rest of the transmission stops a second or two later with a minor, and sometimes not so minor jerk. You always look in your rear view mirror to see if someone bumped you.
My car was checked and I had almost the entire drive train replaced. It seemed to correct most of the problem, but now after a year, the problem is starting to come back. And yes, Lexus says the transmission/drive train is very complicated, doing a bunch of things, so it's not unusual for it to continue doing things at a stop. Hard to believe, but that's exactly what I was told by the dealer.
They say Lexus has a 90% approval rate. Well, I'm one of the 10% who is disappointed. There are a few lemons in every batch, and I was unlucky to receive one of them. Would be scared to buy another one.
I went from my 2003 GX470 to a 2005 GX470 and my new one doesn't have the "clunk" problem. I loved the car when I bought it in 2003 so I learned to live with the clunking when you stop. I drove the car 47,000miles and traded it on a 2005. I trade all my cars no matter what when they hit around 50,000miles. I lost some money during this deal, but I paid the difference for the 2005. Lexus dealers out here in California are very snobby. The only dealer I trust is Crown Lexus even though its around an hour from my home. Lexus Mission Viejo is only 5 minutes, but I always have a problem with them. My wifes LS430 never is in the shop except for oil changes. I can't wait for the new LS460 and the GS450h hybrid.