Hmm... Let me discuss some of the suggestions in previous posts...
Some mention that the McLaren F1 sounds good in stock form. It sure does, but haven't you notice it's the same sample that the Cizeta has? Btw, the Cizeta is the closest car sounding like the real thing... So I would say that the stock exhaust for the F1 is absolutely wrong... There is one exhaust that makes it sound more like a V12... But i'll have to check later. My GT5 file got messed up thanks to the update...
Another one that some are mentioning is the Lamborghini Countach. The old one is fine with the stock exhaust, but the newer one also shares the same sample with the Cizeta... So wrong... I'll have to get this car to see if what exhaust can fix it.
The Audi R8 4.2 sounds good with the stock exhaust. I have no idea if some have noticed, but it's a sample that has been used before in Gran Turismo 4 for the old Audi RS6. It's fine because it's a V8. The Semi racing makes it sound like pretty much every other V8 car in the game.
Another car that people are discussing here is the RX-7. I've only driven the old FD, and it sounds glorious with the stock exhaust. Just what you'd expect from a Wenkel engine. I like the stock exhaust on the RX-8 as well since it still sounds like a rotary, but you can notice the difference between the RX-7's Wenkel and the RX-8's Renesis. I haven't really bothered to try othere exhaust with these. I would expect the sound getting messed up...
As I build up more cars in my garage I'll keep on contributing with the thread...