Wing Commander's background lore has long established that the Confederation includes multiple alien races in addition to humans. We see the Firekkans join in Secret Missions 2: Crusade and Voices of War's history says that "the Terrans, likewise, had befriended several
nearby worlds and quickly assimilated them into the Confederation. All were advanced, but none possessed technology that could rival that of Earth’s." Action Stations has the Kilrathi describe the Confederation including perhaps six additional species ("If they have an advantage it is in their depth, their web of alliances with half a dozen races, the sheer number of worlds they have colonized."). This was 2634, so Firekka would be a seventh if no others joined between then and 2655. The Wing Commander movie and Star*Soldier flags have ten smaller stars on them, which could indicate member species or founding governments. Similarly, there are sixteen large flags on display in the Grand Assembly in Wing Commander IV, which are too few to represent hundreds and hundreds of member planets on their own.
But who are these aliens? With the exception of the Firekkans, they are rarely mentioned or seen, with most productions choosing to describe human extras. Action Stations does mention that young Geoffrey Tolwyn "had met Firekka, Varni, Hagarin, Wu, and others at the Academy", though it's not clear if these are actually member races (the Firekkans certainly were not at this point and the Varni and Wu are both refugee groups fleeing the Kilrathi). With little available specifics, the next suggestion becomes something seen but not discussed on Wing Commander Academy: the series' variety of humanlike characters with unusual eyes and/or skin tones.
Before we continue, it's worth noting that we do not have an answer as to what the intent of the unusually colored characters was. We spoke to Michael Edens who was responsible for the series bible and many episode scripts and he had no idea; his world building work had predated anything visual. It's possible they're intended to be members of other Confederation member species but it's also possible they're intended to be humans in a unique art style, or even some futuristic form of human similar to those in Larry Niven's Known Space who choose new colors or designs for their skin. Of course, no one could ever accuse Wing Commander of stealing something from Known Space!
Lavender Skin, Yellow Eyes
The first unusually colored character we see in the series is Payback, who appears at attention after Red and Blue's opening TrainSim dogfight. She goes on to appear in almost every episode of the series with a particularly major role in Expendable. At one point she does establish that she is from "Icarus colony", but there's no detail as to just what that means. Her lavender skin, yellow eyes and red hair certainly seem to suggest that she's an alien… on the other hand, her full name, Lindsay Price, sounds extremely human. Payback is the only 'alien' that matches her general appearance on the show. She was voiced by Lauri Hendler.
Green Skin, Yellow Sclera
Red and Blue also features a second character who is the only known representative of their phenotype: Hilthros' Flight School Commandant who has a light green skin and distinctive fully yellow sclera. The character seems to be close friends with Commodore Tolwyn, prompting some to suggest he might be intended to be Admiral Banbridge from the tie-in novels. The Commandant is voiced by Earl Boen, better known for his recurring role as a psychologist in the Terminator film series.
Light Blue Skin, Blue Sclera
2nd Lt. Alan "Blizzard" Getz is another character who is seemingly treated as being identical to a human, though his callsign does seem to acknowledge his ice-blue skin, hair and eyes. Blizzard features in The Most Delicate Instrument and he is flashed back to several times later in the show (he's also referenced in The Last One Left as one of the pilots ordered to the briefing room… but he never shows up!). Is he an alien… named Alan?
Light Green Skin
"Raker" is a light green-skinned humanoid with ordinary eyes who appears repeatedly after he joins the Tiger's Claw's complement from the Trafalgar. Additionally, a female green skin character appear as a background extra in both Recreation and Invisible Enemy, the latter of which includes a number of 'alien' background characters. She is boarding the shuttle in Recreation and then attending the funeral and eating at the mess hall in Invisible Enemy.
A variety of background characters with magenta skin and different hair colors appear as pilots in the funeral and mess hall scenes in Invisible Enemy, with a total of nine among the crew eating before the scramble scene!
A single extra in Invisible Enemy has orangish skin and red hair. He appears at both the funeral and in the mass hall. Additionally, another humanoid with the same characteristics (and a very similar face) appears as a pirate ground crew member in The Last One Left.
The unusually colored humanoids are very apparent but there's also another strange one hidden in plain sight. The Tiger's Claw's psychologist, Dr. Guthrig Andropolos, seems to be an ordinary human… except that he's always depicted with blue-within-blue eyes, similar to the Fremen in Dune. This is all the stranger given his connection to the greater Wing Commander history: he's the son of the captain killed during first contact with the Kilrathi and the man who goes on to write the official history of the Terran-Kilrathi War.
While there's plenty of room for debate as to whether or not the unusually colored humanoids are intended to be aliens, there's one that seems much more clear: "Falcon" is a squat pilot with no neck and unusual face markings who seems to be less human and more of a pineapple creature. Like Raker, he's a survivor of the Trafalgar and he appears several times. (Despite his unusual design, his simplified face markings do seem like they could be Academy's style of Doomsday's Maori tattoo).