Totally on the same page regarding favourite season 2 eps (sans one of them - sorry, ol' Boney). I find that my most rewatched episodes are the humorous ones or the extra creepy ones.
My whole family started watching from the beginning (I was only 10 and my teacher was appalled when I said that my favourite tv-show was The X Files, heh) and when Scully got abducted and didn't appear in 3 I was devastated, thinking she wouldn't return. My older brother just scoffed and said, "Eh, Scully's not that important anyway." He just had Mulder on his brain. I considered it a personal Fuck You to my brother when she returned and continued to be awesome and vital to the show.