The Av Club did do a list of ten must-see episodes for the show http://www.avclub.com/article/10-must-see-episodes-of-ithe-x-filesi-82714

I'm not sure I'd agree with all of their choices, but those are all more or less the classics. Maybe a list of the must-watches from each season would be more helpful though, I'm not sure that I'd be able to get into a show if I watched ten completely random episodes, even if they were the best examples of the format. I think that with the X-Files you need to at least watch the pilot for your first episode as it's not a bad episode as far as pilots go, and it does feature Scully's first intro to Mulder and the X-Files, so you're not thrown in there as much