I've only ever had the OE exhaust and the Akrapovic system fitted with the Yamaha panniers, which obviously work fine as they are an approved accessory.

From what I have read, some owners have found that several aftermarket silencers (notably MTC) sit too close for comfort to the plastic backs of the panniers. It is also worth noting that the shorter varieties of silencer, again like the MTC, tend to spray hot exhaust gases directly onto the underside of the Yamaha topcase. There are a few reports of melted topcases.

There is a fix though...

http://www.xt660.com/showthread.php?t=19811

Although I've now changed my panniers to a Holan setup, the Exan X-Black exhaust I have fitted (very slim design) would easily give enough clearance with Yamaha panniers fitted. I reckon it also exits far enough back not to trouble the Yamaha topcase too.

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