Alas, Poor Villain: Valina was an evil bitch, yes, but she seemed to genuinely love the Skeleton King. So watching him kill her without warning and for no obvious reason literally minutes after she had just successfully brought him Back from the Dead is something of a Tear Jerker.
Krinkle was one in a way. Growing up in a lonely childhood, he just wanted to start a family and join the team, but was a bit unhinged and after his first defeat, even more so. A shame because he was a very gifted inventor and could have been a great ally.
Aliens Speaking English: Everyone speaks the same language, reguardless of species, unless they are incapable of speech.
Artificial Limbs: Most notably the monkeys with their robotic arms, which are replaceable. For that reason, the writers have all sorts of fun having these arms torn, cut, or blown off. There's a Running Gag involving Gibson getting his hand cut off at the wrist.
Sprx is usually pretty easy-going, but mess with his friends, and his personality can take a rather scary turn. Take what happened with Mobius Quint, for instance. Calling him Sparky isn't a good idea, either.
Beta Couple: An inversion. Chiro and Jinmay are the ones with the more simplified relationship as opposed to Sprx and Nova.
Big Bad: Skeleton King is behind every Evil Plan and the one in the opening theme.
Big Damn Heroes: Later in the series, The Super Robot exists to fill this role.
Bittersweet Ending: Season 2's finale, with Antauri's death and Chiro becoming monkey-ish. It's made even more bittersweet in the Swedish dub where the series ended after that and was pulled off in such a way that it seemed like a Series Finale.
Bloodless Carnage: The Robot Monkeys are common victims of this, sometimes getting their robotic components mangled while their organic parts remain relatively intact.
Characterization Marches On: Mandarin. First appearence, he's formidible and deviously cunning. Next couple of appearences...there's been a notable drop in his intelligence level... (though having been modified and mutated by Skeleton King might have been a result of that) Though when his clone replaces him he returns to his original characterization a little bit more.
In Flytor, the titular monster takes a genetic scan of Chiro with its eye. We know this is important because we see Skeleton King in possession of the eye with the scan at the end of the episode, but we're not exactly sure how it will come into play until later in Versus Chiro, when we learn that the eye is entrusted to Mandarin to build a factory to create Chiro clones.
The Pit of Doom turns out to be a prominent Chekhov's Boomerang. The first time it becomes important after its introduction is when it becomes the location of Mandarin's cloning factory. But in the Season Two finale, it's revealed that Skeleton King's real intention for building it all along was to reach the egg of the Dark One embedded inside Shuggazoom to awaken it, hatch it, and unleash it on the rest of the universe. And at the end of Season Four it becomes the place where Skeleton King is resurrected. Phew.
SPRX is red, for being Hot-Blooded. Nova is yellow, to represent The Chick (as the show doesn't seem to realize the difference between pink and red). Otto (Mechanic) is green, showing that he's more down to earth, compared to the more scientific minded Gibson (Blue). Antauri is black, as he's more mysterious than any of the rest of the team (switching, later, to silver, to represent that he's extra special compared to the rest). Chiro wears white, because he's The Leader/more important than anyone else (and, also, white light is composed of every color as Chiro has aspects of each monkey's personality), but his highlight color is orange. This is similar to Mandarin, the former leader before his Face-Heel Turn who is also orange, but also represents Chiro's hero worship of the Sun Riders, who have the same color motif.
Almost entirely averted with regard to the relatively few connections between color and elemental powers the team exhibits.
Combining Mecha: The Super Robot itself but it's an inversion in that instead of being separate vehicles that combine into the robot, it's a super robot that occasionally divides into vehicles.
Sprx-77: You know what these strange beacons always turn out to be? Death traps! Always some death trap…
Disney Death: Nova is thrown into a wormhole, Gibson is frozen solid, Otto is eaten, and if Sprx's symbolic death of unwillingly turning evil counts, that makes every member of the Monkey Team guilty of this at one point or another.
Do-Anything Robot: The Robot Monkeys themselves have a wide range of handy gadgets built into them, from power tools to fans.
Evil Plan: Skeleton King has pulled a good number of these, both episodic small term plans and longer terms plots.
Expendable Clone: The idea is played with a bit with Mandarin's. The characters don't treat the clone any differently than they would the original (They might not even be aware he is a clone), but the show itself sure does. The increasingly brutal treatment he undergoes over the course of the plot might have been played a little more sympathetically had he not been a clone.
Eye Beams: Among the Super Robot's abilities, it can shoot lazers from its eyes.
Genre Blind: The Hyperforce. Not only are they willing to accept their superficial victories without any suspicions about what the villain's true goal might be, they are gullible enough to believe even the most obviously suspicious characters. This is Lampshaded by a minor character in Prototype:
Chiro: I know all about you! How you've managed to destroy nearly everything else on this planet! Dr. Takeuchi warned us!
Slingshot: Oh, really? Let's see, were you talking to a human being with a face? Or a disgusting heap of brain on a plate?
The plot of the episode Girl Trouble revolves around Chiro riding around in a small star cruiser with two pretty (and probably older) sisters clad in tight outfits who speak to him in extremely suggestive tones. A "honking" sound effect is heard whenever they move close to him. In one scene, they start to talk to him in suggestive tones again while he is drinking a red-colored soda; he becomes flustered and a GIGANTIC red bubble forms from his nose and pops all over his face. Oh yeah, and Chiro is still in a relationship with Jinmay.
Hand Puppet: In the episode Incident on Ranger 7, Sprx mades a Nova puppet out of an old paper bag.
Infinite Supplies: Downplayed The team makes routine trips to Shuggazoom's moon in order to harvest rocks to convert into fuel for the Super Robot. They were also shown running low on fuel in one instance and had to stop to refuel at an intergalatic truck stop. Other than that, though, the trope is played straight.
Mad Love: Hinted at very strongly for the Skeleton King/Valina ship. Most obviously on Valina's side, and it might explain why SK killed her so abruptly. He was either sick of dealing with her or was disgusted by her weakness or both.
Make Me Wanna Shout: The Monkey Mind Scream, which Chiro, Antauri, and Mandarin are all capable of.
Meaningful Name: Chiro translates to "hero" in Japanese, Sprx uses electrical attacks, Otto is a mechanic and Nova is an explosion caused by a dying star… guess what happens when Nova unleashes her Unstoppable Rage?
Sprx breaks himself with the Fire of Hate, despite Gibson already implying the danger of its power, and helping in the resurrection of the Skeleton King.
By allowing the Citadel of Bone to be destroyed in an asteroid belt, the Hyperforce inadvertently allows Skeleton King to finally separate himself from it, thus gaining the ability to travel and spread his evil around the cosmos more freely.
This led the fangirls of the four monkey males (especially Antauri) to pair themselves up with them by creating robot monkey Author Avatars. Which leads, on the other hand, to loads of Die for Our Ship (or pairing her up with the other male monkeys) towards Nova (if the fangirl pair herself up with Sparx), and a few Crossover Ships.
So Last Season: Black monkey Antauri is reborn as a much more powerful silver monkey during the start of season 3. Face it, he looks so much better in silver.
Space Is Noisy: The team is able to communicate with various things in space, such as Planetoid Q, who probably shouldn't be able to respond anyway.
Spider-Sense: It's not an episode of Monkey Team unless Antauri starts at least one of his lines with, "I sense..."
Stalker Shrine: While exploring the Citadel of Bone, Gibson and Chiro come across a room filled with Chiro's childhood possessions, including his grade school uniform. The following exchange takes place in response:
Undercover as Lovers: In Pit of Doom, Sprx and Nova are forced to go undercover as a married couple in order to trick the Elevator Monster into taking them to the Pit of Doom on the outskirts of Shuggazoom.
Sprx-77: Well sweetheart, looks like your dream has finally come true.
Episode 14 "Skeleton King"- Show us the first true battle against the Skeleton King and his forces. Serves to help hint at whats to come.
Episode 17 "In The Grip of Evil"- What starts as a nightmare turns into an exploration of memories with some bombshells: It's revealed the Skeleton King was once a good and noble man called the Alchemist. Combining magic and science, he created the Monkey Team to stop him from himself
Episode 25-26 "Antauri's Masters" and "I, Chiro." Especially "I, Chiro." We see Skeleton King corrupt the Power Primate and enabling it from helping the heroes while the 'safest place in the galalxy' falls. Furthermore, in "I, Chiro" we see the Skeleton King's true goal: To resurrect a Dark One, calling back to the Pit of Doom. After an intense battle, the Skeleton King is merged with the worm, Antauri sacrifices himself to seal the egg, possibly unlocking the sentience of the Super Robot and restoring Chiro's Inner Primate, turning him into a monkey in the process, resulting in a  Bittersweet / Downer Ending.
Episode 28 "The Savage Lands part 2"- The return of Antauri, the revealed fate of the Skeleton King and Dark One Worm and the Monkey Team's descent into space to end the two once and for all. Also, the reveal of Valina
Episode 49 "Secret Society"- The reveal of two background characters as heads of a Skeleton King-worshipping society as well as being Valina's parents. Also, the Skeleton King's skull reveal into a Crystal Skull, commencing the start of Mandarin and Valina's attempt at reviving him.
The episode "Season of the Skull" is based on the film The Wicker Man (the original, not the remake), right down to The Reveal that the missing child(ren) were in on the whole conspiracy. However, the episode ends on a happy note, in contrast to the film it was inspired by.