Apple AirPort Extremes do several Apple specific things, including acting as a Bonjour Sleep Proxy (allowing other Apple device to sleep and save power but still wake when something else on the network wants to talk to them, such as AirPlay, iTunes Home Sharing, Back To My Mac, and more), supporting Back To My Mac themselves for secure remote administration and file/printer sharing, Mac-style file (AFP) and printer sharing, and Apple's fast/flexible wireless network extension protocol.
They also have higher quality firmware than most wireless routers out there, so they reliably support things that lots of other products don't do reliably, such as proper multicast support, NAT loopback (hairpinning), and they're much less likely to flake out and need to be rebooted.