That's a pretty broad question. There are several PCIe 3.0 cards, and literally dozens of 2.1 cards. Some of the 2.1 cards are faster than some 3.0 cards.
I suspect what you're really after is whether or not the speed boost from PCIe 3.0 is worth it. Well, I'm sorry to say, but there is literally no difference in performance between a 3.0 and a 2.1 link. 3.0 just provides more bandwidth to the card, but cards that need more than 2.1 can provide are literally years away.
A card supporting 3.0 doesn't make it any better than a card on 2.1. Both cards will run at their maximum performance, which depends on a great many things that aren't at all related to which PCI Express revision the card was designed for.