I went from stock to Yoshi carbon fiber slip ons with PCIII, no noticeable difference in sound or performance. Went from Yoshi slip ons to Muzzy 4-1, remapped PCIII to the map they provide for the Muzzy, the change was very noticeable in both performance and sound.
There are plenty of good systems out there. If you are going for performance, don't waste your time with slip ons, go full system. Beyond that it's a matter of splitting hairs and it will most likely come down to price and which one looks best in your opinion. Also consider the noise factor. Yeah some of the louder systems sound great but when you are hearing it for hours on end, it can get a little old, not to mention it could create problems with the local po po depending upon how hard they enforce it in your area.
If money wasn't a factor, I would have a Yoshi full carbon fiber system on my 06. I know a guy that has one on his Gixxer 750, great sound, great look and great performance but also a great big price tag.