I'm obviously a big fan of Millennium and X-Files, but I also liked Frank's Night Stalker remake series. Not sure what to add, so I'll list favorite episodes:
Squeeze, Redrum, Monday, Folie a Deux, Jose Chung's From Outer Space, Clyde Bruckman's Final Repose, Release, The Host, Irresistible, and The Unnatural.
Borrowed Time, The Mikado, Goodbye Charlie, The Sound of Snow, Dead Letters, Seven and One, The Thin White Line, Sacrament, Covenant, Midnight of the Century.
I love Frank Spotnitz...in a completely manly way, of course.