Exo Squad: Alec DeLeon more often than not was The Lancer to squad leader JT Marsh, though Marsala sometimes filled that role as well, depending on the mission at hand. Marsh himself could be considered the lancer to Admiral Winfield, who was the show's Big Good.
Ironically, although being the title character, Sonic was actually his team's Lancer in Sonic SatAM. However, his deeds may also make him the Hero.
Brooklyn in Gargoyles, especially when Goliath promoted him to be his Number Two. He differs in that while Goliath is very physical and direct in his methods with a knack for inspiring his clan, Brooklyn is quieter and more calculating at work as a superb tactician who can organize assaults that seemingly can whup anybody. His only major weakness is that he hates Demona with a fury strong enough to attack her on sight, to the frustration of the clan. Brooklyn is the second type of lancer in that he holds Goliath in high esteem and has no desire to challenge his authority, much less replace him. Still, during the extended time that Goliath was absent, Brooklyn was in charge and old veteran Hudson deferred to his authority and there is no question that he is really good at the job.
The difference in their physiques is probably the driving factor in the differing methods: Goliath can usually get away with being very physical and direct in his methods because he happens to be the biggest, strongest gargoyle available, while Brooklyn is not even half his size and probably not half as strong, so he has to rely more on stealth and trickery as opposed to charging in like a battering ram as Goliath sometimes does.
In the followup Beast Machines, while Primal was absent Cheetor had stepped up to fill the leadership gap, causing him to become The Lancer when Primal returned. This time, it was more the "chafes under his authority, wants to usurp and lead" since he realized that Optimus was slowly but surely turning into a fanatic, and was concerned about the future.
The Optimus of Transformers Animated is younger and less experienced than the average version, so war veteran Ratchet and introverted ninja Prowl can both be seen as foils. Prowl doesn't need to overlap with The Smart Guy, however, and the creators saw him more and more as a second-in-command as his ninja skills developed.
Arcee in Transformers Prime - more sarcastic and down-to-earth than Optimus (who is once again a towering war veteran voiced by Peter Cullen). You could argue Ultra Magnus for the exact opposite reason - Optimus looks Mildly Military next to him.
Rainbow Dash in My Little Pony: Friendship Is Magic is this to Twilight Sparkle. She is widely regarded as the most powerful of all the ponies and is by far the most qualified to lead in Twilight's absence, but normally serves as a necessary foil to Twilight's careful, reflective nature.
On the "modern" team (i.e., after Gibbs leaves) Jodi and Sasha switch off being the Lancer and The Chick. Sasha has the most traditionally Lancer-esque characteristics, but Jodi is polar opposite of The Hero and is the one who goes off on her own while Sasha stays with the group.
Bluegrass. the wingless cowboy, fits this trope, as he uses the main controls of the Miraj spaceship.
Latter member Captain Flashback would fit this as well.
While Longarm of C.O.P.S., may have the many traits of the average American hero, he is no more then a lancer to team leader Bulletproof.
Evangelyne of Wakfu is The Lancer to Yugo. Apart from being several years older and one of the more competent fighters, she's a calm, snarky Tsundere, while he's a cheerful Kid Hero, but with a sense of maturity and responsibility.
Bionic Six has some sort of tossup between the wife (Helen), and the biological son (Eric).
Speaking of Eric from above, the Dungeons & Dragons cartoon has a cowardly caviler by that name.
Adventures of the Galaxy Rangers: Shane Gooseman, the genetically engineered Supertrooper of the is a rare inhuman example. Definitely a little more...questionable in his methods, especially when contrasted with The Hero Zachary Foxx. There's also the fact that Zach is Happily Married while Shane's a Chick Magnet, and that Zach is the eldest person on the team (late 30's to early 40's) while Shane is 19 - barely older than Zach's son.
In the Star Wars: The Clone Wars, even though they are no longer master and padawan, and they both hold the same rank as 'general' during the Clone Wars, Anakin is Obi-Wan's lancer when they are on a mission together. Each Jedi knight has a clone officer as a lancer. Obi-Wan's is Commander Cody and Anakin's is Captain Rex.
In Futurama, in a case of The Hero (Fry) being an impulsive but good-natured idiot with occasional flashes of genius, his Lancer counterpart is the rational, intelligent but hot-tempered Leela.
Vince LaSalle from Recess. While he was never at odds with T.J. (minus the one Feud Episode and "The AV Kid"), the earliest episodes showed him to be more reluctant to join the others' crazy schemes. He's also the "cooler" member of the gang, compared to T.J.'s more energetic tendencies.
Ever After High is a rare example where the protagonist is someone's lancer. Creative freethinker Raven helps Apple- a hidebound traditionalist- to think outside the box and deal with unprecedented situations.