If you can, try and find out the OEM manufacturer of the proprietary batteries made by the camera manufacturers (Canon, Nikon, etc.).
Unless the camera manufacturer also produces their own batteries, the discussion about "non-original" batteries may be moot. For all you know, it could be the same "brandless" factory churning out the batteries.
One set stamped Canon, the other is "brandless". Needless to say the one stamped Canon is gonna cost you 2x or 3x more.
Case in point: when you buy a computer from Dell, exactly which component of the PC is manufactured by Dell? Keyboard - Logitech. Monitor - Viewsonic. CPU - Intel / AMD. Graphics card - some OEM manufacturer. The list goes on.
Even your rechargeable AA batteries... most of it are made by Sanyo and re-packaged, or the technology licensed into other brands.
So my point is, there MAY be a difference between original and 'third-party' batteries, but only if the batteries are made by the camera manufacturer (highly, highly, unlikely, with the exception of Sony perhaps) and the 'third-party' manufacturers are forced to reverse engineer the batteries (and hence such OEM batteries are 'inferior').
Think about it... are Canon or Nikon leaders in battery technology? Unlikely rite... it'll make more sense (and be much more economical) for them to contract out the battery manufacturing process to someone who's actually good at it.