[Spoilers] We’ve got a lot to choose from here. In order of appearance, we meet:
Episode 1, “Rose”: The Nestene Consciousness, a hive mind that can possess plastic as Autons, mannequins come to life to terrorize London. These first appeared opposite the third Doctor, John Pertwee, (Season 8, series 1, 1971)
Episode 2, “The End of the World”: We meet advanced evolutions of earthly species, including trees called The Trees of Cheem (most notably Jabe, played by Yasmin Bannerman, Lute and Coffa). There’s also the Moxx of Balhoon, the Adherents of the Repeated Meme (a plot red herring), the brothers Hop Pyleen (the inventors of Hypo-slip Travel Systems), Cal Spark Plug, Mr. and Mrs Pakoo, the Ambassadors from the City State of Binding Light, the Face of Boe, and finally, not an alien but the last “True” human, Lady Cassandra O’Brien.
Episode 3, “The Unquiet Dead”: The Gelth, a people who have lost corporeal form, crossed a rift in space-time and are animating corpses.
Episode 4 & 5, “Aliens of London”/”World War Three”: The Slitheen, a family of an egg-laying, calcium-based, Raxacoricofallapatorians, (native to Raxacoricofallapatorius).
Episode 6, “Dalek”: The eponymous villain is a genetically manipulated mutant, the (apparent) last survivor of it’s supremely speciesist race, wrapped in a near-impenetrable–if hokey–robotic body. This species has a long Dr. Who tradition, first appearing in “The Dead Planet” in 1963, and cast as the nemesis of all Time Lords, including–and perhaps especially–The Doctor.
Episode 7, “The Long Game”: The Jagrafess, a creature that likes it cold, and controls journalism Satellite 5 and thus all human knowledge.
Episode 8, “Father’s Day”: The Reapers, the apparent riot police of the time-line [with all that term’s 2020 connotations], who try to heal wounds in time and space by killing people.
Episode 9 & 10, “The Empty Child”/”The Doctor Dances”: Not really aliens, but tech; nanogenes try to heal humans, but get the biology wrong.
Episode 11, “Boom Town”: The Slitheen again, the Raxacoricofallapatorians.
Episode 12 & 13, “Bad Wolf”/”The Parting of the Ways”: The Daleks again.
So who wins? Everyone else says Daleks, as they’re a classic Who villain, and they were voted by science fiction magazine, SFX readers in 2010 as the all-time greatest monster–beating out Godzilla and even Gollum from LoTR. And I’m willing to overlook their retro look and embrace the evil of a speciesist race that wants to “EXTERMINATE!” all other sentient life. However, they annoy me to no end, and they are no match for The Doctor. Every time he faces them, he bests them, no matter how many there are. Besides, Lady Cassandra is speciesist too, just less well equipped (and more in need of moisturizing).
On that standard–beating The Doctor–the most terrifying are the Reapers–they’re an elemental force and the Doctor seems out of his league in facing them. The only way we get out of the episode is the death of Peter Tyler. They’re a close second for me, even though they’re new to the reboot–if that matters to you.
The Slitheen/Raxacoricofallapatorians appear more frequently than the Daleks in this season, so they seem a front-runner for best alien–and it’s just fun to say, and to watch others try to say! However, they also are new to the reboot, and they seem to be as much an excuse for situational fart jokes as villains (a key plot device, as it turns out, but nonetheless, juvenile).
My favorites, however, are the Trees of Cheem, particularly Jabe. Perhaps it’s a Star Trek-esque, green-girl thing, but she’s one of the better-developed side characters in the season–she’s wasted on a single episode. Also, an honorable mention to the Face of Boe, who grows on you as the seasons pass, but is disqualified, for reasons we’ll save until later.
So, that’s my two cents. Agree? Disagree? Something I missed? Drop it in the comments.