My daughter's 1995 Accord EX has exhaust leaks. The long pipe in the center of the exhaust system is rotted out.

Where is the best place to order replacement exhaust parts?

Well the dealership will screw you on this one. I'd take it to your local exhaust shops and see what they say. Generally you can always get a cheap custom catback built for under $200. And you can specify what diameter piping you want. That way they could remake a stock one, or you could go larger if you wanted more hp + noise.