Cloudcuckoolander: Quite a few, but Eden is a notable example. Tucker may also count.
Color-Coded Characters: The main group have specific colors that they prefer to wear or are otherwise associated with them.
Tucker ~ Red
Tama ~ Purple
Alex ~ Gray
Logan ~ Yellow
Eden ~ Green
Deirdre ~ Blue
Common Eye Colors: Most of the main group have meaningful eye colors, and many other characters do as well.
Brown Eyes ~ Tucker, Eden, and Alex. This can be easily dismissed as Tucker being Middle Eastern and Eden and Alex being East Asian, but the three of them are the most trustworthy/emotionally stable.
Green Eyes ~ Deirdre and Nell. It conveys both independence and a devious nature, as well as jealousy and sexuality. Note that Nell's eyes are a dark green, while Deirdre's are a paler bluish green.
Icy Blue Eyes: Nathan, on the other hand, is frequently described with icy or cold blue eyes.
Purple Eyes ~ Tama. When attention is drawn to them, she explicitly states that they are simply pale blue that look purple because of blood vessels. However, they do represent her mysterious and regal nature, as well as her supernatural powers.
Eyes of Gold ~ Many Underlanders, who are predominantly supernatural/trickster characters, are described as having gold/amber/pale brown eyes.
Gray Eyes ~ Millicent is described with gray or silver eyes.
Evil Redhead: Nell Greine, who is frequently described as "a super-villain." Her children and granddaughter also qualify, depending on the circumstances.
Extranormal Institute: Slanton School is this, definitely. The strangeness includes regular fights that smash through classrooms, a werewolf as a history teacher, gym classes that frequently involve running for one's life, and an aquitted murderess for a biology teacher (she didn't do it, but it is still frequently mentioned). It also qualifies as an Academy of Adventure.
Fantasy Counterpart Culture: Underland is this, quite explicitly. It is justified by Underland being a splintered world caused by two realities smashing together several millenia ago, and one world floating away while Underland clung to our reality. Despite its age, Underland isn't whole or complete within itself, and thus borrows from the Real World extensively.
This is addressed later in the series, when the vampire goddess Lilith has a nervous breakdown because Underland isn't 'whole.' This prompts her to try to escape into the Real World.
It's also used when Terri kills Phineas, and it turns out the Coven are the pillars holding up Underland. Upon Phineas's death, Underland starts to literally fall apart.
Faux Flame: Traveling spirits frequently appear as Will o' the Wisp type blue flame.
Female Gaze: Deirdre and Shana both have this down pat.
Playing with Fire: A common power in Underland. Deirdre herself is pyrokinetic (though her being a fiery redhead is incidental — her red hair is from her mother's side of the family, while her pyrokinesis is from her father's side).
Unskilled, but Strong: Many of the students, but particularly Tucker's telekinesis. Note that he does become significantly more skilled as time goes on, and soon becomes one of the most (if not the most) powerful telekinetic in the series.
Weak, but Skilled: Many of the students, but particularly Deirdre's pyrokinesis. She has very little actual 'fire power' compared to other pyrokinetic characters, but can do very intricate and advanced moves with small amounts of flame.
What Measure Is a Non-Human?: The purpose of the Hunters is to protect humanity above all else. However, they want to keep the entirety of humanity safe, not individuals.