Nvidia and AMD make the chips and sell them to the different companies. Usually they will make what is referred to as the "reference design", which is their ideal design of a board. Some companies will just buy the reference boards and chips from Nvidia/AMD and slap their logo on it and sell it. These ones aren't usually the top of the line or super over clocked or more memory versions, etc, but a basic card.
The big companies that can afford it, will design their own board, cooling, etc. Sometimes this is aid in overclocking, adding more VRAM, using better caps and voltage reg's, etc. They can also choose what outputs to use, and their design will determine the power requirements, etc. These usually perform better, overclock better and cost most.
Then there is companies that take it even further, like the Saphire Flex cards. With AMD (not sure about Nvdida) but for 3 monitor support to play games on all 3 screens, or more, the configuration as to what ports work and don't work can be a pain. Saphire has designed their own method for doing this that lets you use and outputs on the card you want. It doesn't have to be displayport in the middle, dvi to active adapter for the 2nd or 3rd, can't use VGA, etc. Their Flex cards let you do whatever.