It varies from card to card as to what differences there are between the manufacturers.
With some cards the difference is purely down to warranty and package deal, the actual cards themselves all coming out of the same factory on the same line, and so at a component level being "identical". The early 8800gtx's for example Nvidia had them all made and the manufacturers put them in their own box with their own sticker and added their own warranty. Because I knew this, I went for the very cheapest 8800GTX's I could get at launch (palit) and both cards are still working perfectly now. Normally I go for XFX, as Ive never had any of their cards die on me - despite having a fair number of pcs with them installed at work for a fair few years now.
However some other cards the manufacturers do actually get the boards made themselves and there you could potentially run into quality of component differences between manufacturers.