The X-Files definitely deals with the supernatural, as does Millennium. It's been such a long time since I've seen Farscape, and I haven't finished the last season or the miniseries yet, so I'm not sure.
Should we talk about the big elephant in the room here, Star Trek
? It has employed pseudoscience left and right all the time, but has it been explicitly supernatural? Even the Prophets on Deep Space Nine were explained as non-corporeal aliens.