I for one have never kept the stock motorcycle exhaust on any bike I have owned. The stock motorcycle exhaust gets removed right away or at minimum the cans are gone and new slip on mufflers are put on.
Personally I do this because the stock systems are too restrictive. Due to goverment regulations generally the exhaust system along with the air box restrict the true power that a bike motor can achieve. Much like with cars you will find the most common mods performed are the motorcycle exhaust and the air box.
So how do you decide how far you want to take modifications? I like to push it too where I get the most out of my ride while still maintaining reliability. Generally pipes, a different air breather and a power commander or some sort of plug in fuel injection module which allows me to change the mapping of the bike. You will find those are the most common mods on bikes and also the easiest ones without much impact on reliability but a huge impact on performance.
If you are considering an aftermarket performance exhaust system here are some of the more popular brands that are currently available: Scorpion, Akrapovic, Jardine, Yoshimura, Sampson, and Vance and Hines. You should find a system or slip ons for your bike with one of these manufacturers. Also check out YouTube to find out what they sound like on your type of bike before you purchase.
If you want to drop a lot of weight from the bike a full race system is the way to go. These types of systems tend to drop around 20 to 30 pounds of the bike. Mainly because they are made from light weight materials like titanium or aluminum in order to save weight as well as offer durability.