Off the bat, the grey aliens, the classic big eyed, big headed, spindely limbed beings that became the X-Files default alien depiction do not make this list. They are too, for lack of a better way to describe it, too undifferentiated and ubiquitous to really stand out. They are the "most important" for sure, but hardly the most compelled because of their rather generic nature.
10.) Mars Face- “Space” is widely regarded as one of the worst X-Files episodes of the show’s heyday, if not ever, and the reputation is largely earned. That said, this alien being that was part ghost, part possessing demon was a neat idea and an easy but smart bit of imagery. Too bad none of that made for a good plot.
9.) Alien Spider/Edward Skur- An alien creature, resembling a spider, was surgically implanted into Skur in the 50’s. In the years that followed, Skur would kill for the spider or because of the spider and the creature would feed on the insides of the victims. Skur deepened the mythos by extending the timeline of alien conspiracy into the post-WWII era, showcased another alien that was not a Grey, and pulled Mulder’s father into the story. Also, honestly, just so damn creepy. Yet another example of the ways in which humans were often corrupted, literally or figuratively, by partaking in the conspiracy.
8.) Knowle Rohrer- The obviously “bad” so-called super soldier, Adam Baldwin is essentially the same character he played in ANGEL, just with alien DNA spliced in. By the end of the series, he had become an almost joke of “suspected dead but not really,” but his first few seeming demises led to great and scary returns. His connection to Daggett, however, never managed to humanize that walking cipher.
7.) Shannon McMahon- Rohrer’s arguably “good” counterpart, she is the super soldier who nonetheless begins to doubt the mission and becomes an informant of sorts. Because of Lucy Lawless’s inability to return as planned, McMahon’s arc ends up stumbling to a more tragic and resonant end as she never suffers from Rohrer’s increasingly silly resurrections.
6.) Jeremiah Smith- A healer, Smith is arguably the most vivid and active of the aliens who reject the idea of conquering the Earth or participating in the conspiracy. While Exley’s is more “human” and interesting, he less opposes his alien counterparts plans for Earth and more just opts out of the whole thing. Smith, on the other hand, involved himself in the government in a helping manner (he works, seemingly without much agenda, for the Social Security Administration) and used his alien abilities to heal. A solid character to counteract the tendency for fiction to treat aliens as a monolithic hive mind types.
5.) “Faceless” Aliens- With eyes, nose, mouths, and ears fused to prevent infection by the Black Oil (how the bounty hunters, which the Faceless resemble, were controlled), these guys are walking nightmare fuel by appearance alone. Ironically, the melted features that make them so striking on first glance prevent them from connecting as much with the viewer as the Bounty Hunter did. The Faceless’s activities came as a reminder that although they might oppose the Bounty Hunter aliens, that hardly made them allies of humanity or Mulder and Scully.
4.) Billy Miles- There is a way of viewing the X-Files that makes it the tragedy of Miles, a boy from the first case Scully and Mulder ever work who pops a few other times, each time losing more and more to the aliens until he, himself, is just a disguise worn by an alien.
3.) Lord Kinbote- The alien of a different race at the center of Jose Chung’s From Outer Space is, like the rest of the episode, a delightfully silly over the top creature. Interestingly, however, he is an example of yet another alien who stands up for, or at least derails, other aliens attempts to harm human beings. Additionally, he is animated via the sort of classic Harryhausen approach which is a delight in and of itself.
2.) Josh Exley- An alien who came to Earth and fell in love with baseball and, thus, humanity itself. A sweet story that culminates, sadly, in Exley’s demise but not before it is revealed that his conversion to Earthling was more than skin deep.
1.) Bounty Hunter- Arguably the most recognizable iteration of alien on the X-Files (yes, one could say the greys but they were never given any kind of means to stand out from one another), he is also the most compelling. Essentially, a Terminator dropped into the show—he even resembles Arnold a bit—he unemotionally stalked his prey and was all about unkillable. If you didn’t go it just right, in fact, the wound you gave him would be your demise. A scary, scary dude.