In most cases it's brand name or retailer overpricing. There have been cases where different RAM speeds and the like are used, but that's usually not the case.
Of course, some brands to offer advantages. eVGA seems to be very well liked, since they have dual-lifetime warranty on most cards, and offer the step up program. XFX also has a similar warranty. Also, both warranties allow you to OC and cooler-mod your cards without voiding the warranty.
Myself, I've stopped caring. If I have a 2-3 year warranty, it's good enough. I'll be replacing the card within that time frame anyways. I try to go with the card that has the best cooler. Case in point, the GTX 275 I just ordered. The stock cooler looks like this:
I ordered this one instead:
It might not look as cool, but it's a much better cooler. Heat pipes + dual fans and better ramsinks means that my card will run both cooler AND quieter than any stock GTX 275 out there. I generally tend to think that a better cooler is preferable to a lifetime warranty.
