It's not a big price difference, but it's still something worth considering.
Sometimes, you can even find USB adapters on sale for half that price. Mini-ITX motherboards are even worse most of them only feature a single PCI slot, making a USB WiFi adapter all the more important. Micro-ATX motherboards usually only come with 2-3 slots.
You may not want to waste an extra slot on your WiFi adapter if you plan on connecting a lot of PCI devices, such as graphics cards, sound cards, Firewire cards, RAID cards, TV tuner cards, or so on.
