Curse Quest: Minerva to the Owl Hunter. Minerva seems to be much more capable than the Hunter, but is still considered his apprentice. The Owl Hunter believes he took down the owl-bear, even though Minerva one shot it with her energy-tipped arrows in a few seconds.
Baliir of Drowtales, to Kiel. Who outright acknowledges he basically keeps the whole mess she rules over running and working.
Sidekicks: Back when he was a Sidekick, Darkslug was this to his master hero Dunkelheit despite the hero being considered the strongest superhero behind Guardian. So much so that while Guardian easily defeats Dunkelheit in combat, Darkslug actually ends up defeating the superhero.
Noblesse has lord Raizel & his battle butler Frankenstein. Sidekick Frankenstein does the bulk of exposition, the science, and a huge chunk of the fighting. Hero Raizel is almost devoid of personality. All we know about him is that he drinks tea, eats ramen, and doesn't make facial expressions. He always shows up at the last minute to save the day in mere seconds after every other battle capable character is exhausted.
The premise of Sidekick Girl, though the title character is not happy with the status quo.
In Anti Hero For Hire, Union was a Hypercompetent Sidekick for Dr. Nefarious before breaking out on his own.
Erfworld: Wanda Firebaugh fills that role for the overconfident and strategically inept Lord Stanley.
And for protagonist Parson Gotti, who's a strategic genius but needs a crash course in the rules of Erfworld.
Likewise, Parson plays this role in a strategic capacity to Stanley.
Richard from Looking for Group is the most powerful member of Cale's team, being able to kill with his hands or use magic do perform whatever execution he has come up with for his enemies. Tempered a little in the fact he is an evil undead warlock and hinders the group as much as he helps them with his crazy antics, recklessness or beating up Cale for fun.
Redcloak from The Order of the Stick is the sidekick who makes Xykon's evil organization run. Although Xykon is devastatingly powerful and capable of surprising cunning at times, he has no patience for details, and his idea of strategy consists of pounding obstacles with spells until they go away. It helps that Redcloak is Genre Savvy whereas Xykon suffers from Contractual Genre Blindness.
The prequel book Start of Darkness establishes Redcloak as having elements of a Beleaguered Assistant. Throughout the webcomic itself (especially the later strips), more and more of this pokes through to the surface. He still voluntarily works for Xykon, though.
Somewhat voluntarily at least. It's partly that that keeps him working for Xykon, and partly because he doesn't want the death of his brother to have been a complete waste.
Judy, the Doctor's receptionist, in The Adventures of Dr. McNinja. While Dr. McNinja is competent in his own way, Judy's dependability and no-nonsense attitude are pretty much the only reason anything gets accomplished in the office. She's also a gorilla. Just thought that should be out there.
"Do you think I run around with a twelve year old boy just because I like his inferior grasp of girls and higher level math? Do you think I left him with my psychotic parents because I wanted him to die? No, you undead pale ponce! Gordito is the effing badass kid. So go ahead and finish up your masterful scheme to make me let you kill me, because Gordito's going to slap around whatever ghost lackey you have like he was a pinata on the Mexican day of the dead."
Rose Lalonde from Homestuck is this to the main protagonist, John Egbert. She appears to be much more mature than her other friends, and also is a pro at Sburb compared to John.
To some extent, this is true of all the leaders seen in the series. John is quite derpy, Karkat is overwhelmed by almost constant rage and self-loathing, Jane is overly skeptical and distracted by romantic angst, and Kankri spends far too much time explaining what he perceives to be discrimination. Being a leader in Homestuck seems to rely more on caring about other people than any skill in leadership.
Dr. Wily was tricked into becoming the hypercompetent sidekick for Mike Haggar's in Captain SNES: The Game Masta. When President Haggar's first act was to abolish taxes, Vice President Wily realized he'll be too busy fixing Haggar's horrible decisions and keeping the country afloat to take advantage of his position.
Partly deconstructed in Girly, where sidekicks engineered to be perfect become too much so, rendering the "hero" of their relationships virtually unnecessary. However they end up evil, try to take over, succeed, and have to be taken out by pairs of hero/sidekick pairs of roughly equal ability or the more typical competency ratios.
Also Otra APPEARS this to Winter, but it's been proven that Winter is what inspires Otra to be so competent and both are far weaker/more helpless alone. Otra, in general, can do everything by herself but would hate to and Winter can kick ass, but needs Otra around to be able thanks to Rule of Funny/Rule of Drama.
Elliot, Dr. Breign's assistant in The Snail Factory. He essentially does all of the work, cleans up after Breign's messes and keeps everything going.
Bun-Bun from Sluggy Freelance. The other characters still have to take care of things themselves most of the time, since Bun-Bun is a Sociopathic Hero who won't lift a paw unless there's something in it for him and/or the current bad guy did something to piss him off. However, when he does get involved, heads tend to fly.
Bill the Extra Guy is the sidekick to Fred the Spanyard from Neglected Character Comix, a Sprite Comic series involving Mario characters on the Neglected Character subpage of Super Mario Bros. HQ. A seemingly useless sidekick compared to Fred's death rays and other such powers, he freezes time and space with his "extra power" which leaves his friend more than impressed.
Last Res0rt has Adharia Kuvoe's servant and consort, Sedja the Efreet. Sedja is essentially a Benevolent Genie, but is bound to and protected by Adharia (as it's been heavily implied that Sedja would've been destroyed by the Star Org if not for Adharia protecting her, acting as a translator, and having hidden her up until the point Sedja was shot out of a pistol).
Namine serves as one to Governor Zexion in Ansem Retort. Given Zexion's habit of blowing the state budget on things like explosives, hookers, and Doritos, Namine is frequently the one organizing things so that the government doesn't collapse on itself.
Jasomet from the sequel to Elijah And Azuu (Pre-Teen Demon) could easily solve the lead characters' problems, but he's stopped partially by his Literal Genie mindset, and the fact that the other characters object to his graphically violent methods.
Captain Kaff Tagon of Schlock Mercenary has several, depending on the situation. Normally it's Kevyn, but on more specialised subject (medical, legal, etc.) others step in.
Stand Still, Stay Silent: The Västerströms are the actual figureheads of the expedition, but have no experience dealing with people outside the academic field and have relied on their military acquaintances Taru and Taru's friend Trond to actually build a viable expedition plan, especially when Cutting Corners became a requirement. Taru and Trond also brought in four out of the five actual crew members that were picked among their various acquaintances, when all the Västerströms had to offer was a nephew who happened to have dropped out of the academic field to join the army.
A story arc in Questionable Content introduces Tilly, who is trying way to hard to be this to Hannelore. Tilly seems to actually be hypercompetent, the problem is they're trying to prove themself to someone who doesn't actually want or need an assistant, and won't always take "I don't need you to do this" for an answer.