Back when I wrote about issues with Canon-brand batteries and Canon chargers, I mentioned that many third-party batteries, even if they have higher capacities, do not last quite as long as the genuine versions. Dave Dugdale of Learning DSLR Video wanted to find out if a third-party LP-E6 battery (in this case Watson), would last as long, or longer, than a genuine Canon version. Here are his results:
Even though it makes sense that the Canon might last longer since it's capacity is slightly higher, if the two were equal in performance, it shouldn't be a full 20 minutes longer -- and the Canon battery is a year old! This has been similar to my experience with third-party batteries, but I have not performed a scientific test. I think what it comes down to is that you should weigh the price vs. performance for what your usage may be. Many monitors that can run on LP-E6 batteries, like the SmallHD models, take two batteries, so it may actually be worth it to buy a number of cheap ones as you're going to be using two anyway. If you're using them in a DSLR, you may prefer to have the genuine Canon batteries so that your camera can stay on longer and you can switch batteries less.
When it comes to charging batteries, I think for most productions people are charging whenever they need to charge (whether fully depleted or not), so even if you wanted to follow the recommendation of either company, it just may not be feasible.
What have your experiences been like with third-party batteries? What are your charging habits for Lithium Ion like these?