Former Trope Namer Radar O'Reilly, especially in seasons 1-3, where he was running things for the somewhat overwhelmed Colonel Blake. Later seasons had the more efficient Colonel Potter, so Radar didn't need to be quite so Hypercompetent. Lampshaded in the season two premiere, when a general says that it often seems as if Col. Blake is Radar's clerk.
After Radar's departure, Klinger, originally a complete incompetent, grows into the role as part of his character development but is never quite as hypercompetent. Father Mulcahy notes that Radar had a similar start before growing into the Hypercompetent Sidekick he eventually became.
This is the popular perception of The Green Hornet, due to Bruce Lee's later popularity and the fading of the Green Hornet himself from pop culture. Although Kato gets the impressive fight scenes, the Green Hornet is still portrayed as the competent leader.
Buffy the Vampire Slayer: Although Buffy is by no means incompetent, Willow does a great job of personifying this trope in Season 7, when as the most powerful witch in the Western Hemisphere, she was so strong that the writers felt the need to knock her out before most major fights.
Walter Harriman from Stargate SG-1. He doesn't do all of the work at Stargate Command, but he has been compared to Radar. Wasn't he named after him?
Major Marks turned into the Walter of Earth's battleships in both SG-1 and Stargate Atlantis. He's served on all five of the Air Force's ships (usually whichever one is being used by the main characters at the time).
On the villainís side the First Prime of Lord Yu did a good job of compensating for his masterís increasing madness and senility.
Jennifer, from WKRP in Cincinnati. Played with in that Jennifer is both the highest-paid member of the staff and the one most respected by Mrs. Carlson, the station owner.
Bernard Woolley, Jim Hacker's PPS in Yes, Minister, who finds his loyalty split between Hacker (who badly needs his help to decipher the Civil Service red tape) and his Civil Service superior Sir Humphrey (who expects him not to tell Hacker anything that might disrupt the status quo), and usually chooses Hacker.
On the semi-rare occasions when Hacker and Humphrey are on the same side, Humphrey is this.
In Remington Steele the apparent "boss" (Remington) is explicitly a figurehead for PR purposes and Laura is the one who is, in fact, in charge.
Baldrick is normally thought of by fans as a classic Bumbling Sidekick. Yet in the first season of Blackadder Baldrick was a Hyper Competent Sidekick. And as mentioned above, Blackadder was the Hyper Competent Sidekick sidekick in the third season.
In The Adventures of FATMAN, the Show Within a Show in The Weird Al Show, Fatman's sidekick, Harvey, despite having no superpowers and being a hamster, can talk and is generally more quick-witted than Fatman.
Al Borland from Home Improvement is a hypercompetent sidekick, but only on the Show Within a ShowTool Time. Tim really is a mechanical genius, but lets his reach exceed his grasp in the same way that the speed of light exceeds a highway speed limit. Tim's inventions usually fail because they are too powerful, causing them to either explode or work too well, such as a vacuum cleaner that doesn't so much clean the dirt out of the carpet as much as it cleans the carpet out of the room. Whereas Tim embodies Awesome, but Impractical, Al embodies Boring, but Practical.
This becomes reversed when the two guest host a cooking show together. Al is the far superior cook, but Tim's inferiority complex at being upstaged by Al's abilities causes him to study hard and learn how to cook decently. Al, for his part, does not like being corrected by Tim and makes similar mistakes to the ones Tim usually makes.
In Episode 5x20 of Star Trek: Deep Space Nine, Rom and Quark's mother Ishka becomes the lover and assistant of Grand Nagus Zek. Her importance isn't revealed until later in the episode, when Quark is forced into the position and finds that his mother was keeping the Alliance afloat.
While Avon is far from incompetent, Stringer Bell in The Wire is much more cool-headed and business-oriented while Avon sees himself as primarily a "soldier".
Leslie started off as an analogue of Michael Scott from The Office, but the writers eventually took her in a different direction, so that by Season 3 she is acknowledged to be brilliant at her job and respected by a lot of people in Pawnee because of it. (Although she is the protagonist of the show, she is in fact a sidekick, the Deputy Director of Parks and Recreation under Ron Swanson who is pretty much happy to let her run the department.)
Sgt. O'Rourke from F Troop, who also runs a saloon and an Indian souvenir business under his commander's nose.
Stiles on Teen Wolf. The protagonist Scott is more brave than bright, and relies heavily on Stiles to do the thinking. With his ADHD and general geekiness, it would seem like he should be a comic relief character, but Stiles' intelligence and bravery makes him indispensable to the usually clueless Scott. In fact, Stiles is so useful that Scott has to share him with Derek on the sidekick front.
Laura, the leisure center's assistant manager in The Brittas Empire. Every time she's left in charge, business booms...but it all goes back down the pisser as soon as Gordon Brittas gets home.
Charlie Young in The West Wing. Not that the President is incompetent, but still, he needs all the help he can get.
Mrs Landingham too, to an extent, until her death in season two. Charlie's comment to the president about why he always had a good quality pen in his pocket comes to mind.
Also Leo to the President, Josh to Leo, and Sam to Toby.
Major Dad gave us Gunnery Sergeant Alva "Gunny" Bricker.
Merlin is this to Arthur, so very much. Though Arthur is by no means incompetent, how many times has Merlin secretly saved him from an almost certain death? If you factor in the episodes in which he does it multiple times, it's practically a Once per Episode occurrence.
Morgana gets her own in Agravaine. While she's an extremely powerful sorceress and he's not, all she seems to do is sit in her hut and cook up the next evil plan to settle her latest petty vendetta. He actually infiltrates Camelot, basically has the king doing whatever he wants, and hands her Camelot on a silver platter while she snarls at him about how horribly he does.
They also seem to be the only ones aware of each others' skills, as Merlin is the only character who takes Agravaine's manipulative talents seriously and Agravaine is the only character who seems aware that Merlin is only pretending to be dumb to hide his intelligence. They basically spend the fourth season telling their respective bosses "He's not harmless, he's dangerous, and we need to get him out of the way" and being ignored.
Francis got a hyper competent assistant in one episode of Malcolm in the Middle. He ended up so reliant on the assistant he was unable to function on his own. Fortunately, the assistant fired himself for him.
In C-drama The Holy Pearl, High Priestess Mo Yin is this for the King. When he goes AWOL, she makes sure he has sufficient guards; she throws his brother out on his ear after he attempts a coup (twice); and she governs the realm until he comes back.
Truly is this in Bunheads despite her own serious emotional issues
"I know what everyone needs except me"
On Spin City, Mike Flaherty (Michael J. Fox) for Mayor Winston.
Patrick Jane, the title character on The Mentalist, is technically only Agent Lisbon's sidekick: she carries the gun, makes the arrests, etc. But her clearance rate wouldn't be nearly so high if she didn't have Jane around.
JAG: Bud Roberts when conducting research or finding witnesses. He had that role regulary in seasons 2-4, and on occassions afterwards when sitting second chair or likewise.
Starfleet is supposed to be an entire organisation of these in Star Trek, as you have to be the best the Federation has to offer to make it as far as being a cadet. Though it obviously varies from person to person.
Discussed in Star Trek: The Next Generation. Riker is repeatedly offered his own command, and everybody from Starfleet Command to Picard thinks that Riker is ready to captain his own vessel a few seasons in. Riker prefers to stay on the Enterprise because that's where the action is.
Hinted at with Jadzia Dax in Star Trek: Deep Space Nine. As a Joined Trill, she has over half a dozen lifetimes of memories and skills to call upon, not to mention being a master of Klingon martial arts and possessing Ph Ds in multiple scientific fields that she achieved both before her Joining and before turning thirty. She's happy to stay as the station's Science Officer, even though she clearly competent at commanding a starship. Sisko and Kira often turn to her for advice.
Julian Bashir turns out to be this too.
Spock to Kirk, and likewise Data to Picard. Both are magnitudes more intelligent and mathematically/scientifically capable than their captains, but their lack of emotional empathy often makes Kirk and Picard better suited to the situation at hand.
MastersOfSex — Virginia Johnson is this to Dr. William Masters. He has the credentials and tenure, but she has the organizational expertise.
In Chuck, the titular hero is this to whoever is the manager at the time. In his case, it's because he's an Almighty Janitor. It becomes apparent early on that Chuck is really the one who runs the Buy More.