Above Good and Evil: Merklynn's only desire is to see magic restored to its former prominence. As such, he doesn't care one way or the other about whether or not his agents are good or evil, so long as they perform the tasks he gives them. At the start of the series, he would also bail out whichever side needed his aid, in order to keep his agents in play (setting captured Darkling Lords free, for example). However, after one too many attempts by Darkstorm to steal his power, Merklynn decided to start letting the Darkling Lords get themselves out of trouble. He also became friendlier to the Spectral Knights over time, and took action against legitimately evil sorcerers.
Animal Motifs: All the characters (both Spectral Knights and Darkling Lords) have an animal symbol (called a "totem") that grants them their powers. They also represent the emotions of the users.
Additionally, the staves had dual-image holograms (one image unique to each staff representing its power and the other representing the owner's affiliation). The Spectral Knights' staves had a unicorn, while those of the Darkling Lords had a dragon.
Arch-Nemesis: Cryotek and Cindarr. Galadria and Virulina. Ectar and Reekon. They all knew each other before joining their respective factions.
Bad Powers, Bad People: The Darkling Lords all have totems based on creatures that, In-Universe, seem to have unpleasant symbolism at best (in addition the array of predators and scavengers, there's The Brute with a Killer Gorilla form, the Yes-Man who becomes an innocuous skittering beetle, and a cowardly figure whose form is vaguely armadillo-like). Beyond that, their power staffs consist of three based on Destruction, Decay and Fear, and Lexor's, which is implied to be based on Cowardice.
Good Powers Good People: In comparison, the Spectral Knights have noble animal totems and far more benevolent-themed power staffs, such as Knowledge.
Barrier Warrior: Lexor's power staff allowed him to erect an impenetrable protective barrier.
Colour Coded Armies: You can tell the character's alignments just by looking at their armor. Bright primaries for the Spectral Knights, and variations on black, red and purple for the Darkling Lords.
Additionally, the totem animal images on their chests; the Spectral Knights had blue images, the Darkling Lords had green.
The Spectral Knights' weapons and staves are silver and the Darkling Lords' ones are gold.
Continuity Nod/Running Gag: The Botanical Garden Committee. Other lesser examples include the barracks zoning problems and the farmers from "Quest for the Dragon's Eye" being accused of "unfair competition".
Dangerously Genre Savvy: Darkstorm has proven to be quite cunning and probably wrote a page or two of the Evil Overlord List. For example, he is perfectly willing to help others, as long as it furthers his goals, such as saving the other Darkling Lords in the first episode in exchange for their servitude. He even chastises Virulina for her selfish attitudes regarding others.
Virulina:"I, for one, would never try to rescue one of my friends.
Darkstorm: "That, my dear, is why you have no friends".
Designated Girl Fight: Galadria, the female Spectral Knight, is able to turn into a dolphin. The only member of the Darkling Lords she can fight happens to be Virulina, the woman who turns into a shark. Oddly averted with Virulina herself, who got into a few fights with the male Visionaries and did fairly well for herself.
Hypocritical Humour: In Lion Hunt, Leoric is Mode Locked in lion form (with a Palette Swap so he looks like a different magical lion) and is being hunted by his own friends because the commoners complain that there's a lion terrorising them. After the truth has been revealed, the commoners call their powers "witchcraft" and the Knights tell them not to jump to conclusions without learning what's actually going on. Leoric gives a rather sarcastic growl.
Inferred Holocaust: Technology stopped working. We see a plane crash and 10 years later the huge (technically still habitable) cities are abandoned despite the fact that there is no way that the villages has enough room for all the people who used to live in them. Clearly there is no longer any need to provide housing for millions of people.
Jerkass: Merklyn is a complete and total asshole. The first episode ends with him making the people he just empowered leave via mudslide, while he points and laughs, for no reason other than his amusement. At one point he threatens to blight the good guy's kingdoms if they don't obey him.
Monochrome Casting: The entirety of the cast is made up of Caucasians — the only people of any other race are seen in background group shots. Even the cancelled second set of toys features exclusively white guys.
Mystical Plague: The Magical Plague in Horn of Unicorn, Claw of Dragon only affects magic users.
Never Say "Die": While "destroy" is used, "slay" is also fairly common. Very averted, however, in "The Lion Hunt", in which every Spectral Knight says "Dead?!" unbelievingly, as the presumed fate of Leoric. Darkstorm even tells his allies to kill the villagers!
Only in It for the Money: Lexor only served Darkstorm because Darkstorm paid him. At one point, he even mutters to himself that he'd willingly serve Leoric if the Spectral Knights made him a better offer.
Royals Who Actually Do Something: Leoric (Prince of New Valarak), Cryotek (King of Northelia) and Arzon (Crown Prince of Regalia). On the Darkling Lords side we have Darkstorm (Ruler of Blackdak), who usually takes a personal hand in trying to defeat the Spectral Knights.
What Kind of Lame Power Is Heart, Anyway?: Of all the totems Merklynn could have chosen for Galadria and Virulina - they get stuck with aquatic animals. They also end up with neither Staffs (until the comic book series), nor Vehicle-based powers.
Also invoked in-show by Ectar when he compared Leoric's Staff of Knowledge to Cindarr's Staff of Destruction.