Dave Dugdale from Learning DSLR Video tested a factory Canon LP-E6 against a Watson LP-E6 after market battery. He found that the Watson may have a chip built in since his EOS-5D Mk III can register it and track the performance. Unlike the Canon manual, stating the battery can be recharged anytime, the Watson instructions says to recharge only when the battery is dead. This indicates the Watson battery has less charging cycles.
In his tests a new Watson LP-E6 lasted 1 hour and 9 minutes while an one year old Canon LP-E6 battery lasted 1 hour and 28 minutes. One has to be careful when buying third party batteries and parts. Canon has a consumer page on their website discussing counterfeit accessories.
Personally, I have bought third party batteries for my non EOS-1 camera bodies but I stick to very reputable companies. However, in the last few years, I have bought all Canon factory batteries because as a professional wildlife photographer going on frequent foreign trips, batteries and memory cards are so critical to a successful shoot. Extremely cold weather can affect the performance of batteries. When I was in the Arctic photographing wildlife in -20 degrees Fahrenheit temperature, I discovered the LP-E4N battery in my Canon EOS-1D X came through with flying colors.