By now, the pattern of almost all X-Files seasons is established: mythology episodes at the beginning and end of each year, with a couple of double-episode mytharcs mid-season. In between, the monster-of-the-week eps, and some lighter fare, are spread around.
The show's third year is consistently strong, and high-quality. It seems odd now to look back, having watched all 9 seasons- at the time this series seemed mature even though it was barely a third of the way through its run. The season finale, Talitha Cumi, even when viewed with the season 4 opener Herrenvolk, isn't top flight, but the rest of the season makes up for it.
Clyde Bruckman's Final Repose, Nisei/731, Piper Maru/Apocrypha, D.P.O., Pusher
Episodes I remember not liking, but enjoyed this time round:
Teso Dos Bichos - famously disliked by cast and crew. Not as bad as I remember, but not good.