Mu La Flaga is The Kirk in Gundam SEED, but interestingly it's Murrue, The McCoy, who fills the role of The Captain on the Archangel with Sergeant Rock Natarle, The Spock, as her second-in-command; he is more pragmatic and emotionally thicker-skinned than the idealistic and inexperienced Murrue, but more laid-back than Natarle and more capable of seeing past military regulations than she is. Mu's influence as a mediator between the two is felt most strongly in the first parts of the Archangel's journey, before Murrue gains confidence in herself as captain.
Meowth of Team Rocket in Pokémon, although they're all pretty much on equal footing (early in the series, however, Meowth claimed to be the leader of the Trio and this may be why). Meowth typically subverts this by wholeheartedly agreeing with whichever one of his teammates happens to have the same ideas in mind he has.
Hikaru in Magic Knight Rayearth fills this role. She's the closest thing to The Leader that the group has, with a cooler head than Umi and a more gung-ho attitude than Fuu. She's especially affected by the end of the first half and ends up taking one hell of a third option to fix the Pillar System at the end of Part II by applying the power to everyone.
I'm not sure that this works. Luke is more the naďve farm boy (The McCoy) and Han the more sensible, pragmatic one (The Kirk, since he says Kirk-like things such as "Never Tell Me the Odds") but there isn't really a Spock-equivalent. Obi-Wan is less cynical than Han, and Leia abandons the entire Rebel Alliance just to save Han in Episode VI.
Luke does became The Kirk, but only in Return of the Jedi. Because he has controlled emotions. For example Obi-wan told him that he has to kill his father in order to bring peace, but Luke a logical suggestion that maybe he can be saved because Vader didn't kill, and if was truly evil he would have killed him. His leadership skills have also improved over the last two movies.
"McCoy in a way represents for us, or represented for us, the extremes of The Kirk and The Spock. If Spock is extreme logic, ... extreme science, and Kirk is extreme emotion and intuition, here you have a very colorful doctor, essentially a very humanistic scientist. So he, in a way, is literally and figuratively a representation of two extremes that often served as the glue that held the trio together."
The Avengers: Iron Man fits The Kirk, and Captain America fits The McCoy. Given that Thor is calculative and likes control, and that Banner (when he's not Hulk) is calm and logical, either one could be The Spock.
Tobias in Animorphs takes this role whenever he's alone with Marco and Ax.
What do you mean? Out of the Animorphs Marco and Ax are the two most logical. Both are occasionally given to bouts of emotion overwhelming logic (understandable seeing as they're both teenagers) but out of the group they're definitely both closer to The Spock end of the scale than The McCoy end.
A better example from Animorphs would be Jake, with Rachel and/or Cassie at The McCoy end, depending on whether the story is about saving things or killing them.
In Smallville, Chloe Sullivan often fills this role between Lana and Clark.
The Doctor has fallen into this trope so far, he can no longer be deduced as either an anti-hero or anti-villian. He will give his life (but has not been able to, yet.) to save anyone, any race (minus the Daleks), and planet, or any specific cascade inspired by certain snake haired monsters of Greek mythology from an alien race known to exterminate any other race... You get the idea.
Believe it or not, Jack O'Neill of Stargate SG-1 wasn't really his quartet's Kirk; that honor fell to Samantha Carter and occasionally Daniel.
Which makes Carter a good fit for the new leader in Stargate Atlantis, replacing another Kirk figure, Dr. Weir. The leader of the main team, Sheppard, tends a bit toward The McCoy-ish in his thinking, though he does have the Kirk-ish role in picking the proper course of action out of McKay's stream-of-consciousness TV Genius-ness, Ronon's rashness, and Teyla's more McCoy-ish tendencies.
Sheppard fully ascends to Kirkdom in the last season. Woolsey is The Spock, while Teyla & Ronon are The McCoy.
Mal in Firefly can be pretty emotional and amoral in his own right, but has the virtue (much as he'd deny it) of listening to his crew before making a decision, but being brave enough to take unpopular decisions regardless.
Lee Adama in Battlestar Galactica usually brings the moral clarity to situations where other characters' judgement is blinded by prejudice or fear.
When he isn't blinded by his own prejudice and fear, that is.
Carly in iCarly, the centre of the trio that includes The Spock like Freddie, and The McCoy-type Sam. In iDate Sam & Freddie where Samantha and Freddie start dating, she ends up having to solve all their fights, until the end where it becomes too much and she tells them if they can't stop fighting they shouldn't date at all.
John Crichton from Farscape went from being The McCoy to The Kirk, while D'Argo and Aeryn started out more The Spock and became Kirk-ish as they went along. Pilot is probably the purest Kirk character on the show.
On JAG, the role of the Kirk alternated between Harm and Mac.
President Wayne Palmer in 24 was The Kirk to Tom Lennox's Spock and Karen Hayes' McCoy and found their differing viewpoints useful in his decision-making process.
Teen Wolf: Scott fits this trope. Scott displays leadership qualities and is the one who has the ability of bringing people together to work for a common effort.
Ben himself is The Kirk alongside Gwen and Kevin, especially in the first season. Strangely, Gwen and Kevin barely fit as the The McCoy and The Spock respectively (both are intelligent and emotional) and can switch the roles depending on the situation. By Ultimate Alien it's hard to peg any of the three as any one of the archetypes, though Ben is definitely the The Spock in the season one finale since he decides Kevin has to be stopped by any means necessary and The McCoy Gwen is trying to save Kevin from himself.
Mr. Bogus himself qualifies, as he most often provided the balance between his younger cousin Brattus and his best friend Tommy Anybody.