We've been at WDW for several Father's Day. There has never been anything special except once in awhile a CM will say, "Happy Father's Day".
We too make our own celebration. Usually he gets the souvenir of his choice. Last year, he bought a really nice watch at DTD. We usually eat someplace different. This year we are eating at Boma for the first time. He is very excited about this. I also try to get a pic with his favorite character.