These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Canon Sue: Thorn gets seen as this by some fans; she's destined for greatness, gets New Powers as the Plot Demands, and is often more of a focus than the title characters. However, it's pretty clear she doesn't fit that definition; although she might have powers, she makes many mistakes and bad judgements, is constantly hurt and injured, and only succeeds thanks to the help and support of the rest of the cast. Keeping in mind that the comic was originally called Thorn, this is not as big a surprise as it might have been. She's pretty much the actual main character, with the Bones serving as First-Person Peripheral Narrator (Fone Bone in particular, who was the Ishmael in his Moby-Dick dream.)
Ho Yay: Not uncommon in the Bone fandom. Usually it's either with Smiley and Phoney, or Fone Bone and Phoney. Where's Smiley and Fone Bone, then? A far less common one is between the Two Stupid Rat Creatures, but it is more joked about.
I Am Not Shazam: The name Bone doesn't actually refers to a certain character in the story - that happens to be the name of the species of the three main characters Fone Bone, Smiley Bone and Phoney Bone. (Keep in mind, the surname Bone is also shared among many others of their kind, if not all of them.)
Jerkass Woobie: The villagers of Barrelhaven are foolish, gullible people who are easily led into mobs, but it's hard not to feel sorry for them considering the sheer hell they go through once the real conflict starts. Wendell in particular, despite being a jerk many times in the past, constantly seems to be on the verge of a nervous breakdown as he endures the war.
It's a little hard to not feel at least a bit of pity for Kingdok as he suffers an ever-worsening Humiliation Conga over the course of the series. He once was a mighty king of the Rat Creatures, and was even willing to live in peace with the valley-dwellers and stay in the mountains. His clan was taken over by The Hooded One and he was forced to obey every command given. By the end of the series, having lost an arm, his tongue, been smacked by rocks, and bruised by stumbling around in the dark underground, he's actually demanding Thorn kill him rather than having to go on living the life he's been reduced to.
Hell, the entire Rat Creature race counts. According to the Two Stupid Rat Creatures, they were happy to just leave peacefully in the mountains and honor the treaty and didn't start acting evil until the Hooded One showed up and started manipulating and controlling them (Kingdok in particular; the Bone wiki even describes him as a slave puppet) into going to war. As Smiley points out, the Hooded One basically corrupted a fairly peaceful race into a warlike insect cult.
Memetic Mutation: "Stupid Stupid Rat Creatures!" became one in the early days of the internet.
Moral Event Horizon: Kingdok eating Thorn's mother alive. Kingdok even points out that it's a Moral Event Horizon in his attempt to get Thorn to kill him. It doesn't work until he bites into her leg to impede her progress.
When The Hooded One and Tarsil face off, she casts an illusion of his old, handsome face. The real Tarsil's face is so mangled that his look of shock is barely discernable even as she rushes him and cuts him in half at the waist before he can react.
Kingdok and the other Rat Creatures have pretty nasty moments given their featureless eyes and rows of teeth. Even the two Stupid Rat Creatures get a few creepy moments before their bickering sets off.