For aftermarket accessories, I usually go to 4wheelonline because of their good service and pricing. Actually, I just ordered a set of dually wheels for my 3500HD.
I agree. It depends on your budget also. Try to check out 4wheelonline. They have inexpensive exhausts like Gibson. If you are willing to spend more money, Borla and Corsa have some great sounding cat-back exhaust systems.
Check out also the Undercover tonneau. I bought the Flex cover and have been very happy with it so far. Easy to install, and it is pretty water tight. I don't have a large tool box in my truck bed but I have the Undercover SwingCase which is enough for my tools and other small stuff.