With Freecom's USB 3.0 hard drive ready to ship in November, and many more USB 3.0 products expected in 2010, it looks like USB 3.0 is going to be the most popular connection for peripherals in the future. There are a lot of peripherals that will never need the performance of USB, so they may continue to use USB 2.0, but since USB 3.0 is backwards compatible, it will also work for USB 2.0 devices. So I think more and more motherboard manufacturers may start including USB 3.0 ports.
Even though FireWire-800 has been around for awhile, I haven't found any included on any motherboards yet. These manufactures will probably stop including any FireWire ports - IEEE1394a or IEEE1394b) in future motherboards. Actually almost all of the new small form factor, higher performance mini-ITX motherboards don't include a FireWire port. The future doesn't really look to bright for FireWire.
Some people say USB became popular because a lot of PC systems and peripheral manufacturers did not want to pay licensing fees to Apple for FireWire. So they conspired to develope USB. Sure it wasn't as fast, but for a ot of peripherals, it was fast enough. Then USB 2.0 came along and provided much better performance. Many argued that it was still not as fast as FireWire for things like external hard drives, but for many people it was fast enough. Now USB 3.0 may make the need for FireWire totally obsolete. Except there is that little issue of cable length, which still gives FireWire an advantage.
But maybe USB isn't the perfect solution. I haven't heard of anyone using USB for display devices. Monitors are connected with DVI, HDMI or DisplayPort.
Now we've learned that Apple has pushed Intel to develop a new fiber-optic connection for peripherals called Light Peak. Light Peak could be a solution for just about every PC peripheral. It could replace all the cables we currently use for monitors, external drives, printers, scanners, audio interfaces, etc. Distance isn't a problem, at least compared to FireWire, because a Light Peak cable can be up to 100 meters long. So, will USB 3.0 become the most popular way to connect peripherals? Maybe not.