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.
Complete Monster: Medusa. The way she abuses/manipulates everyone, including her own child, who she sees as nothing more but an experiment, manages to completely counter the fact she is an incredible Magnificent Bitch. Unlike most examples of this trope, though, Medusa is able to feel love, although her love just makes it even worse. Just ask Stein or Crona, both driven to madness by her affections.
Too many examples to list. Suffice it to say that if you go three episodes without seeing something that qualifies, you aren't watching Soul Eater.
Black Star certainly qualifies. He constantly straddles the line between this and Too Dumb to Live. Slams squarely into the former, however, during the Rescue Kid arc. G.O.O.'s attempt to make him crazy just makes him more awesome.
While the Meister/Weapon pairings undoubtedly have their fans, there is quite the sizeable fandom for Kid/Crona... it doesn't help that it would probably come just behind Stein/Marie in the Hurt/Comfort department.
Don't forget Maka/Crona. Whether it's het hurt-comfort or Les Yay hurt-comfort, they still have their fans.
And Soul/Maka. To the point where Maka/Crona vs Maka/Soul could be a Base Breaker. Both have several points of canon and rabid fans.
Fan Yay: Free, probably due to being hairy and muscular.
Stein seemed to do this intentionally to squick out Maka when he was pretending to be a bad guy. He referred to her soul as "cute," and commented on the smoothness of her skin.
Justin and Giriko could also count as well, since the anime portrays them as rivals.
Giriko admits he has some for Maka. Considering he was a girl by then, it also counts Les Yay. Let the Interplay of Sex and Violence begin only for it to end immediately with a literal rage death
Germans Love David Hasselhoff: In Italy, apparently it was so popular among the scanlations-reading fans and such that the manga was translated and published because of it, and was quite popular for a long time. The fact that the anime was translated and aired uncensored (it's actually one of the few Italian dubs to include Precision F-Strike here and there) probably helped.
Crona's a boy! Crona's a girl! CRONA'S A BOY! CRONA'S A GIRL! BOY! GIRL!!! BOY!!! GIRL!!!! BOYGIRLBOYGIRLBOYGIRLBOYGIRLBOYGIRLBOYGIRLAAAAAAAAAAAAAARGH! *tears hair out*
At the end of October 2009, FUNimation's reveal of the English voice for Black☆Star on YouTube garnered near-500 comments in 8 hours of people arguing about how bad her voice was! Way to go, FUNimation. 'Bet they'll think twice about posting previews of their voices online from now on. (Poor Brittney Karbowski, tho.)
Jerk Sue: Black☆Star. Although he's a jerk throughout, he has Jerk with a Heart of Gold moments towards the beginning that make up for it. As the anime progresses though, he continually does dumb things, but anyone that tries to point them out either gets called out for being a jerk to Black Star, or they change their mind. The two worst cases would be episodes 33 and 38: in the former, Black Star's arrogance throws off the Chain Resonance, something stated directly by Stein himself, but Maka is called the problem when she tries to call Black Star on it; in the latter, Black Star blows off everyone, acts like more of a jerk than normal, and challenges Kid to a duel just so he can prove his power to himself after failing so many times... and Sid and Tsubaki let him off when Maka tries to stop it, saying it's just the way he is and they have to accept that.
In the first opening, at one point Blair is seen jumping on a table in Maka and Soul's apartment with the whole gang over. Maka is disgusted/annoyed. Tsubaki doesn't seem to know what to think. Death the Kid and Black☆Star freak out, Soul gets a nosebleed. Patty and Liz, who were right near blair, appear to be pleased with what they see.
Medusa, the Knight of Cerebus in the series, she subverted the usual Dark Magical GirlHeel Face Turn by turning Crona into The Mole, succeeded in awakening the Kishin, only "lost" to Stein and Death Scythe because she won, took over the body of a small child so no one could attack her without hurting the little girl, drove Stein to madness (the not funny kind), outed a good witch who just wanted to defect, and is leading Shibusen against her rival with Shinigami-sama's blessing.
And her Magnificent Bastard Quota keeps rising exponentially! Turns out, the whole reason behind leading Shibusen to defeat Arachne was so Medusa could steal her sister's gorgon body when she abandoned it to become madness incarnate, and to try and kill Maka, who's Demon Hunter wavelength apparently poses a threat to her and the entire witch world. Also, as of the new chapters, she is manufacturing FAKE MADNESS CLOWNS from information she got from Shinigami and Arachne. Yeah, she's pretty much the boss of this trope in this series.
His name is Soul Eater. And he does. With great pleasure. And nobody sees anything wrong with it.
As for him, so for the other Weapons. The manga more so than the anime mentions that while there are rules about which souls can be eaten, the origin of these rules—Shinigami-sama—makes the whole business arguably suspect depending on how you view the Dumbledore-ish Eldritch Abomination Grim Reaper. Mifune, for example, was said to be a legitimate target despite his peculiar circumstances (He only fought to protect Angela, a witch too young to be a threat to Shibusen or anyone else).
At least this is the case in the manga. In the anime, Mifune is never suggested as being a target of soul collection. It's more an issue of the fact that (as of the Arachne arc) he works for the villain, so they were allowed to kill him if necessary, but taking his soul was off limits. In the manga, though, Shinigami-sama totally suggests that Black☆Star should take Mifune's soul, as well as Angela's, right from the very beginning. (Though, to be fair, it's implied that he only suggested it because he knew Black☆Star wouldn't do it.)
Crona might just be the woobiest woobie that ever woobed.
He may be the biggest one, but he's far from the only one. We have Maka with her massive insecurities, Soul with his inferiority complex (manga only), Tsubaki with her brutal sibling problem, Liz and Patti with their Dark and Troubled Past, Stein with his constant struggle to keep sane, Eruka with her forced servitude to Medusa under threat of death, heck, even Ragnarok could qualify (see Fridge Horror above).
Villain Sue: To people who don't gush over Medusa's Magnificent Bastard status, she is this, always having a Xanatos Gambit ensuring her victory and having extreme luck in some situation, like her constant avoiding death.