I have only seen POF once. POF is much easier to terminate than copper and will eventually replace it. It is more expensive than Cat 5 and comparable in costs per foot to Cat 5e. POF is about 30% cheaper to install than Cat6 and about 60% cheaper than Cat 6a. Just like plastic PEX pipe is replacing copper in our homes it will eventually change networking.
The automotive manufacturers love POF and have been using it for 20 years but it is gaining commercial and residential popularity. They also use a safe red or green light as opposed to a retina burning laser.
Cat 5E cable is rated up to 350 MHz while POF is rated in the real world up to 1,250 MHz and double that in laboratory tests. Higher frequencies equal higher bit rate throughput.
I still use Cat 5e copper because I am familiar with it and like Mark said you will have to update parts of your cabling structure to convert to POF. I would consider POF on a brand new install.
Cat 5 - 100 Mbps - 100 meters (328 feet)
Cat 5e- 1 Gbps - 100 meters
Cat 6 - 1 Gbps - 100 meters, 10 Gbps over 50 meters
Cat 6a - 10 GBPS - 100 meters