"War of the Coprophages" certainly had one of the best endings ever
. But personally I liked "Syzygy" better. I loved the banter between Mulder and Scully. And the scene in which they fight over who gets to drive the car was actually a hint to the fans. Apparently fans were complaining about Mulder always being the driver when the series was still on.
I wanted to comment about the other episodes, too, but it somehow slipped my mind. I remember that I saw a video in which Carter said that "Oubliette" had some parallels to a real abduction case - although not on purpose. But the fact that there is very little supernatural going on about the abduction itself makes the whole episode very real... and very creepy. The binding between the kidnapped girl and Lucy almost ruined it for me. Almost
As far as the mythological episodes are concerned I am not a huge fan of them, but in season 3 they are at least still halfway decent. I found it very weird that all women from the abduction group still had their implants. But the part with the bomb was really great.
Mulder sees what looks like Aliens and they are only just lepers that were part of the WWII experiment.
I don't remember that. I thought it was not properly cleared up and left to the imagination of the viewer whether or not the alien was actually a real alien.