Base Breaker: Howard. He's either a funny character, or an insufferable Jerk Ass with Skewed Priorities. Not helping with this is part of the fandom's tendency to excuse his worse moments as "just part of his character" while leaping on Randy for the slightest jerkish inclination (though this has lessened recently).
Julian, the goth boy, is a very popular character within the fandom.
His popularity could be a contribution to him becoming an Ascended Extra in the form of his Evil Doppelganger, Shadow Julian.
Morgan, the leader of "Dancing Fish", is another very popular character.
The Tengu has a huge amount of fanart.
Theresa is ridiculously popular for the amount of screentime she's had, to the point where there are several Ninja Theresa AUs and other fan ideas with her as the protagonist floating around the fandom.
Rachel, the clarinet girl who is also a big fan of the Ninja.
Evil Is Cool: In-universe, Randy and Howard would love to boycott McFist's products but they're just too cool for them to pass up on purchasing them.
Slips into Fridge Brilliance when one realizes they'd stick out if they stopped buying things from the most beloved man in town.
Ho Yay: The relationship between Randy and Howard runs close to this a lot.
Season two ramps it up by having an episode where Randy gets jealous of Howard hanging out with Bucky (titled "True Bromance") and where they have to take care of a bologna "baby" for science class and bicker over who gets to look after it.
Moe: There's no sugar coating it-Randy is adorable.
Rachael may be this In-Universe, so of course some people in real would feel the same way.
Julian could possibly be the best example, being the perkiest Perky Goth ever and having a cute appearance to match. The soft voice (courtesy of Dee Bradley Baker) helps.
Moral Event Horizon: Shadow Julian crossed it when he controlled Howard's mind and had him walk towards a pit, giving Randy a Sadistic Choice to either stop him or save Howard.
The Sorceress. She only appeared for two episodes and hasn't even been mentioned since making her an Aborted Arc.
Theresa and Debbie due to being rather popular among fans and even getting some focus episodes, making them prime candidates to move into a Main Character slot, but they always end up pushed back into the background after the episode focus is done.
Heidi as well, as she is the girl who appears in the most episodes with a speaking line, but is usually just dumping info on the setting.
Like above, it's most of the female characters including Morgan and Rachel.
Despite playing a major part in the Evil Julian arc, some fans feel there wasn't enough focus on Julian. Specifically, he was stuck in a shadow dimension and there was a bit of filler during this arc, meaning that most of the focus still went to Randy and Howard despite Julian being a driving force.
In general, many new villains outside of the Sorcerer, McFist and Shadow Julian (Mac Antfee, Catfish Booray, the Sorceress) only get two episodes about them before their plots are resolved, which is too soon in the eyes of many fans.
Viewer Gender Confusion: Julian, to some, due to his androgynous appearance and quiet voice. The fact that he's partially inspired by Noel Fielding-who also falls under this sometimes-doesn't help much.