Depends on the card, game/benchmark and what version of PCI-E were talking about (1, 2, or 3)
Worst case scenario, a GTX680 loses 27% of it's performance using a PCI-E 1.1 slot at 4x. A HD7970 in the same scenario loses 14%.
Today's PCI-E 3.0 slots at 4x have as much bandwidth of a PCI-E 2.0 slot at 8x, which is just fine. http://www.techpowerup.com/reviews/Intel/Ivy_Bridge_PCI-Express_Scaling/24.html