The Final Fantasy video game series features repeated incarnations of Those Two Guys, invariably named Biggs and Wedge after two minor characters from Star Wars (tropes that the names link to are tropes of the Star Wars characters).
The Turks would also be a good example, Reno and Rude acting much like a comedy duo in The MovieAdvent Children.
An especially weird example occurs in Kingdom Hearts where Donald and Goofy objectively fill this role as "normal" characters, despite technically being much more well-known than the Squeenix-born characters.
Selphie fills the role to a T in the second game (Tidus and Wakka are only mentioned). She shows up to talk to Kairi and then... obscurity. Yeah.
Fire Emblem will have two ordinary Social Knights/Cavaliers travel with the main lord of the game. They generally are not in charge, important, or in any way special. (The exceptions being Oscar from Fire Emblem 9, and Kent and Sain for Fire Emblem 7.) The pair were just chosen to protect the Prince/Princess when plot happened. They are always sharply contrasting, they have no late game dialog or importance, you could let them die at any point. They are a recurring theme for the series, one of the knights wears red, the other wears green. Generally, any dialog with one has the other in it as well (except for certain one-on-one dialogs that happen later on).
Fire Emblem 9 has Oscar and Kieran, who do not appear together when you first meet them. However Kieran has a not short dialog with Oscar showing them to be another example of this trope. Since Kieran is a self-obsessed duty bound ignored self-proclaimed rival, and Oscar is a laid back relaxed friendly guy who wonders what crawled up Kieran's backside.
9 also features Janaff and Ulki, the Hawk King's retainers.
Fire Emblem 13 has a similar exception in the form of Sully, the red knight of the game who can marry the main character. Considering she's one of a whopping four (five if you have a female Avatar) girls said character can romance when most of the other units can pair up with anyone, that says something.
Fire Emblem 10 has Edward and Leonardo, neither of which is a knight, but both members of La Résistance at the beginning of the game. True to trope, they quickly disappear from the plot, but with an interesting subversion: when everything is quickly going to hell for Micaiah and she's doubting her choices, they appear for a quick scene that drives the point home that the whole country, including her old friends, are trusting her to be always right.
Sometimes we get Those Additional Two Guys, generally a pair of axe users (one wearing blue, the other brown): Ward and Lott in the 6th game, Bartre and Dorcas in the 7th.
Both Osu! Tatakae! Ouendan and Elite Beat Agents usually feature two team members that stays constant whenever the difficulty changes, except during the hardest difficulty (where everyone gets replaced by girls). They usually follow their current leader and not the one who did most actions (they did, but not as big as the leader, who also does most poses, especially the rivalry poses in Ouendan 2). Their names:
Ouendan: Atsushi Saitou and Ittetsu Suzuki (Red team), Tsufushi Moriyama and Kenshin Sugita (blue team).
Elite Beat Agents: Agent Derek and Agent Morris.
And even the girls have their version of this trope. There's Aoi Kanda and Anna Lindhurst (Ouendan red team), Honoka Kawai and Reika Minazuki (Ouendan blue team), Agent Missy and Agent Foxx (Elite Beat Agents)
Xenosaga has The Professor & Assistant Scott, a pair of Super Robot otakus trying to make it in a Real Robot world. In the first two games they only play a part in optional sidequests, but in the third they are integrated into the main plot, joining the crew & even rebuilding KOS-MOS into her final form.
Huey and Rostam in Treasure of the Rudra. They die early on in Sion's scenario; their bodies however are controlled by Surlent when he dies several days after the incident and goes out to reclaim his own body.
Persona 4 features Kou Ichijo and Daisuke Nagase, a.k.a. The Fellow Athletes..
Hanako and Taro in Disgaea 2 and Asuka and Lillian in Disgaea 3. Taro and Hanako lampshade it in the final chapters when, noticing that the game is now Shooing Out The Clowns, realize that they are thoroughly lacking in serious motivations (Taro, for example, is tagging along because he thinks Rozalin is hot) and proceed to make some up on the spot.
Xzar and Montaron from Baldur's Gate are supposedly foreign spies, but this vaguely promising premise is not followed up on at all. Xzar in particular is such a useless character that players have been known to kill him deliberately to make room for someone more interesting. Their purpose seems to be simply to bulk out the party until you meet some of the better characters, and it's assumed in the sequel that you ditched them at a fairly early opportunity.
Unless, of course, you're evil, in which case you hang onto them and ditch Khalid and Jaheira. Coincidentally, they also happen to have pressing business in Nashkel, so if you're not interested in picking up Khaleid and Jaheira, you will get the breadcrumb.
Corporals Mike and Anton of the Washington National Guard in World in Conflict make it all the way from the attack on Seattle, through the nuclear blast in Cascade Falls, then back to the liberation of Seattle. They don't play ANY role in the story at all but their reunion after getting separated in Cascade Falls just has to make you shed Manly Tears.
Gabriella Daniels and Kenneth Donnelly in Mass Effect 2, though it's actually "Male and Female Crewmen". They play the trope extremely straight, though. Every time you're down in engineering to speak to Tali, the two have one of their endless banters, that include many of the games best jokes.
In Mass Effect 3 there are Privates Bethany Westmoreland and Sarah Campbell, two of the the Normandy's guards, who are always commenting about your missions.
Smart Guard and Dumb Guard are arguably this in the Thief series.
From the Brothers in Arms series you have Allen and Garnett. It's even mentioned that most people refer to their two names as all one word, and that they're never seen apart. They even die together.
Though their appearance is brief, Griggs and Sheckley from Half-Life 2: Episode Two definitely qualify. Better yet, one of them is Adam Baldwin.
The two guys both marked as "Gossip" in Dragon Age: Origins, who show up in every town and chat about rumors in the game, whatever quests you've already completed, and random stuff such as how one of them banged the other one's wife.
World in Conflict has Mike and Anton, two corporals from the Washington National Guard who get roped into the whole mess.
In the Regime Universe of Injustice, you get shades of it with Regime Flash and Shazam. They aren't Dragons like Wonder Woman and Yellow Lantern, but they're typically fought against together and can be found together in scenes. The point is driven home when Regime Superman murders Shazam, which causes Flash to jump ship and help the Insurgency.
This can also be seen with Regime Cyborg and Regime Raven, but this is fairly obvious because they're both Teen Titans. The last two living Titans in that universe, in fact.
In Resident Evil: Revelations, Quint and Keith, aka "Jackass and Grinder" certainly qualify. Their constant jabs at each other, immature behavior, and humorous banter definitely make them two of the most memorable (if not likable) characters in the game. Possibly the whole series.
Captain Tsubasa games has Amaral and Douter, a pair of Brazillian wingbacks who are always together, both in and out of your teams.