Funny. I started watching at season 1 thinking that the show wouldn't survive 1 season like most Friday night sci-fi shows (see Strange Luck, Firefly, etc., etc.). I liked it right off, but when they did the movie they started writing stories that separated Mulder and Scully a lot to accommodate the film shooting schedule, which I thought was bad for the series--and that trend didn't seem to improve much even after the movie was finished! Then, instead of throwing in the occasional funny, quirky story (which was good), they were trying to do it all the time, which I thought was bad for a series that was supposed to creep you out. So I started to watch less. I must have been one of the few who welcomed Robert Patrick's arrival (Try not to be too angry with me! It wasn't his fault Duchovny left!) because I watched more the last couple of seasons as they increased the number of creepy stories again. I know, I'm in the tiny (!) minority because most people loved Mulder so much! 'Course, I wasn't a big Duchovny fan or M/S shipper, so there wasn't a big disappointment factor for me when Duchovny decided to leave the series.
Me, I probably liked the first season the best, although there are classic episodes scattered throughout the years, even in the seasons I liked the least.