Yes, there is a difference with some filters. Whether fuel or oil filters, you should stick with Ford stuff, or it's equivalents Fram and Racor. If you have an International dealer nearby, check there. They are usually cheaper than the Ford dealer. I've gotten awesome deals on Ebay and diesel sites that have classified sections. The last deal I got, was for two Motorcraft oil filters and two sets of fuel filters for $85, from a guy who sold his 6.0. I don't mind having a bunch on hand if they can be had for a good price. Don't buy off shore filters if you are keeping your truck.
The Hauler - '05 F-350 4x4 CC Dually 6.0 Powerstroke
The Project - '90 Ford Bronco 4x4
The wife's - '11 Ford Escape
For every minute you are away from work...you can add two minutes to your life!