I'm up to Darwin's Eye. After about a 1/3 or so of the way through Season Three, they seemed to drop the cop show aspect a little bit and go for more of a supernatural feel. As I said before, looking back the episodes aren't as 'bad' as I once thought. They're the weakest of the series but they're still not as bad as their reputation might lead you to believe. TEOTWAWKI, Closure, Skull & Bones, Borrowed Time, Collateral Damage, Matryoshka, Saturn Dreaming Of Mercury are all pretty good. Omerta and ...Thirteen Year Later (their attempt at Darin Morgan) were both alright. And I think The Sound Of Snow stands with some of the best episodes of Millennium.
I like The X-Files episode only because you get to see Frank Black reunite with his daughter as the new millennium begins. When I heard that that episode was happening, I was sure that they weren't getting into the Millennium Group so I wasn't too surprised/dissapointed when the episode had almost nothing to do with the series. The one thing that irked me was that Skinner says that the Group disbanded a few months ago. They had existed for hundreds of years and suddenly right before their big date, they just fall apart and disband. What kind of cult is that?

I think 1013's days of TV are over. Maybe someday Chris Carter will get another show going but, as Bill mentioned, Carter currently seems to be more interested in movies. That Ted Serios script has been around forever.
They sure as hell had a great run and I'm happy it's ALL on DVD. Now onto The X-Files sequel!