I haven't looked into third-party batteries for my 5D MkII yet, but I have experience with third-party batteries with my Rebel XTi (NB-2LH). I use a brand called "Ultralast" and they are far superior to Canon's batteries and ONE-THIRD the price. Canon's version is rated at 720 mAH, and the Ultralast is 950 mAH. While many battery manufacturers' juice ratings are suspect, these ones deliver.
I tried at my local camera shop first, and they offered Optex's version, which the camera shop guy said lots of them had trouble with because they crapped out after a few months. I can't vouch for that, but they were only one-third less than the OEM Canon batteries, which is too expensive when you can get two for that price (or three for the price of one Canon). I go to a dedicated battery store for all of my batteries. (You can do as well with cell phone batteries: 50-65% LESS, better performance.
Anyone who ignores third-party batteries is cheating themselves out of money and performance.