Clip-on are usually lower then stock and attach directly to the forks. This gets you lower on the bike and out of the wind. Also depending on the bike can give you a faster steering input and better feedback from the front tire. I went from the stock bar on a GS500 to clipons and it made a huge differance. As Tony stated that are cheaper to replace then stock ones.
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Team Pro-Motion Safety Director/Coach #23
As stated prior, they get you lowen on the bike, usually. Be aware you must have adequate clearance to mount a lower and sometimes wider bar. Non faired bikes shouldn't have a problem. I tried clip ons on my 929 and even with race bodywork, you can't go lock to lock with the forks. The bras would have to be mounted so far back, you couldn't hold them properly and they would hit the tank and crush your hands.