The Michael Emerson Brady Bunch episode and Burt Reynolds is God episode in season 9 weren't too bad. I liked the William episode too.
I actually thought season 8 had some solid mythology episodes (that season 9 kinda retroactively made worse by muddying up the alien replicant plot into supersoldier bullshit). Plus, Vienen was a very solid black oil story that was basically the only time the show teamed up Mulder and Doggett.