Battery PACKS (as opposed to just individual "Batteries") are, like most electronics, getting smarter all the time. I agree that none of the camera manufacturers manufacture batteries, but I think some of the "Packs" are starting to contain electronics to monitor the overall condition of the pack, regulate the voltage, and/or just identify the pack as being OEM. Whether the 3rd-party manufacturers are able to replicate that I don't know. I don't know if the camera manufacturers even care since it's such a relatively small market.
I have used a 3rd-party pack twice. Once was for a camcorder that I bought for my office. I ordered the camcorder along with an extra battery pack since it was going to be on job sites for most of the day. The aftermarket battery pack literally would not even go into the camera since there was a tab on it that prevented it going into the battery housing on the camera.
The other time was when I bought my first DSLR. I got a second battery for it and didn't realize at the time that it wasn't a Nikon battery. No big deal, it fits the camera, the ampacity is higher, the voltage is the same, and it works fine. Over time I started to see the difference. Both the Nikon pack and the aftermarket pack were charged more or less the same number of times however the aftermarket pack began to lose ampacity rather quickly. After a year or so it fell off during use much more quickly than the OEM pack did.
Long story short: I stick with OEM batteries in my cameras. The aftermarket packs usually work, they usually perform as they are supposed to, and they cost a bit less. When I buy a Nikon pack I don't have to worry about the "Usually" part. I know they will work properly, and that's worth the difference in price to me.