Big Ol' Eyebrows: His final art design used these. Before then he had no eyebrows except to emote.
Charlie Brown Baldness: His design for the first two seasons had only four long hairs coming out of his hat, even though his High Score design had thick blond hair. His altered form in "Project 2" and "2 Fast" and his later design from season 3 on revealed that his hair was supposed to be blond.
Chick Magnet: In High Score (before Bonus Stage), Joel was presumably June's boyfriend (she's much less acknowledged in Bonus Stage), but even in Bonus Stage, Joel's the object of Elly's affection, he starts dating Jessica, and then it's later revealed he has an ex-wife.
Cloud Cuckoolander: Many of his "inventions" were pretty out there, even for being a mad scientist.
Joel: Well, on some scale, collar crooks, find the terrorists, improve the economy... but mostly I just intend to mess with peoples' lives, which is far more fun.
Pirate: He claims to be, and in two episodes, he acts like one.
Joel's roommate and straight man.
The Alcoholic: More of an Informed Attribute, as his alcoholism is brought up a lot more than he's ever shown actually drinking. But it is brought up quite a bit.
Butt Monkey: While other characters are killed mercifully or quickly, Phil is more often killed slowly and painfully, screaming the whole time.
Dogged Nice Guy: If he's trying to be nice to someone, expect it to backfire.
Informed Deformity: Phil is treated as horrifically ugly, especially by women, despite not looking appreciably different from any other character. As with many character traits in the show, this is increasingly forgotten later on.
In her first episode, the characters don't realize she's a robot until she speaks.
Apparently, Craig didn't realize she was a robot, even after their (clearly robotic) son was born.
Fiery Redhead: Mostly just snarky in the second through fourth seasons, but she gets aggressive towards Evil before being shut off in "Evil's New Groove", and she goes through a killing spree in "Joel vs. the Monobrow".
Jerk Ass: Hates pretty much everyone, and it shows. Later in the series, she arguably delves into Jerkass Woobie territory, what with her desire to become human and all.
Killed Off for Real: In "Ryaconning", she dies due to being in real human form when she is stabbed by the Cloaked Figure.
Pinocchio Syndrome: Later on, she expresses a desire to be a real human in the real world. Eventually fulfilled, but she dies soon after.
A former classmate of Joel, Phil, and Elly. Was known as Hat Boy in grade school.
Early-Bird Cameo: Appeared as "hat boy" in a flashback in episode 61, "Fist World", before her first appearance as a non-extra in episode 71, "Joel Goes to College".
Love Makes You Evil: According to Word of God, Cassidy was the cloaked figure from episode 79—her motivation behind killing Rya (and, had the series continued, attempting to kill Elly) was that she viewed the other girls as threats to her potential relationship with Phil.
Murder the HypotenuseHer attempts to do this caused the events of "Ryaconning" and would have driven season eight.
Nice Hat: Which was apparently her defining feature as far back as grade school.
Only One Name: While all the other major characters have at least had their surnames alluded to in some way (such as Rya's being shown as Botkins in the credits to one episode, and June's being shown as Crane in High Score), Cassidy's is never mentioned, not even as a joke.
She Is All Grown Up: She was known as "Hat boy" in grade school because no one bothered to ask her gender.
Stalker with a Crush: Attracted to Phil enough to try, and in one case, succeed in, killing others she views as a threat to their relationship.
Yandere: She initially seems sweet and level-headed, but her apparent Stalker with a Crush feelings towards Phil and the fact that she killed Rya as a result could definitely place her under the Yandere heading.