Well, first of all I'd like to say Hi Spadea! And I hope you feel at home here :-)
Hmmm . . . I can't think of just 5 to pick!! There's so many good ones!!
My favorite eps in no particular order are Beyond The Sea,
Squeeze/Tooms, Colony/End Game, Anasazi/Blessing Way/Paper Clip, Clyde Bruckman's Final Repose, Grotesque (no one else liked it that much, but I LOVE it when Mulder does his "getting into the criminal's mind" thing! They need more eps like this one!) Pusher/Kitsunegari, Syzygy, Small Potatoes (LOL!!! This ep was so funny!! I think DD did an exellent job of acting in this one!!), Demons, Tunguska/Terma, Paper Hearts, Momento Mori, Gethsemane/Redux/Redux 2, Kill Switch, Bad Blood, The Pine Bluff Variant (no one liked this one because it wasn't an actual X File but I thought the suspence and the drama in this one made it one of the best! But that's just my opinion though :-) ) Folie A Deux, Arcadia, Monday, The Unnatural (DD has a talent for writing, don't you think?), and finally, last but not least Biogenesis/6th Extinction/Amor Fati.
Geez, I think I just managed to give myself a severe case of writer's cramp! But I think I got them all :-) Or at least the REALLY good ones!