Shout Out: Masamune's shadow, as well the one as in Tsubaki's and Masamune's dreamscape, the elongated stick figures seem to be references to the horror short manga The Enigma of Amigara Fault (Drr... Drr...). Also, Soul's mindscape (as well as the imp in it) is a reference to the Red Room from Twin Peaks.
In Episode 1, just after Blair is revealed to be a cat, Spirit Albarn says "A cat will do!" in his smarmiest voice. This might just be a reference to a certain Tsukihime fan-comic that gave rise to the "A cat is fine too" meme.
During the same chapter Ox makes a reference to Kim, who he recently learned was a witch, as being an angel. The discovery of the band Angel Witch, and their song of the same name, adds yet another point to the long list of music references Atsushi Okubo makes.
Capone, the first villain encountered by Black☆Star, ends most his sentences with "...you know?", which is the closest you get for an english translation of "dattebayo". Possibly unintentional.
In episode 17 (Excalibur's second appearance), there is a part where he is speaking to Ox about how he could no longer find any satisfaction. We see him walking through the very same street that is depicted in the cover of David Bowie's The Rise and Fall of Ziggy Stardust....
There's another direct reference to David Lynch in the episode right before the scene with Excalibur talking to a woman on a cliffside, with a shot-by-shot remake of the shadowy swooping shot of the Mulholland Drive street sign, taken directly from the same film.
The most recent chapter has Maka attempting to ride Soul in his scythe form (with a drastically shortened blade) and they try to manifest wings from the back to fly, though, as Maka complains, the wings are anything but angelic.
The second attempt is tiny but at least not as spiky as Soul's imagination seemed to be making them initially. The third, powered-up by soul resonance, is much larger and noticably angel-like, as with Maka's soul.
The manga even seems to have a shout out to the Iconic ending of the anime. Clearly, when Maka punches out her opponent in Chapter 65, her fist is packed with courage!
Interestingly, just before Maka kills her, Arachne comments that courage * isn't* enough to win every battle. She then got bisected by Demon Hunter, but even so...
Shouts to numerous works of fiction and myths
Episode 43 of the anime features a sort of Theme Park Version expy of Prypiat, complete with the iconic Ferris wheel. However, it swaps the Chernobyl reactors for a MacGuffin guarded by a pair of robotic clown... things.
Is it just me or does Noah look a lot like a Noah?
Watch the 3rd ending at about 1:15 and tell me what you see. I'll give you a hint: Envy
Not just her, but the statue/creature below her looks a lot like Gluttony too.
Incidentally, the Book of Eibon comes from Clark Ashton Smith via HP Lovecraft. The curious might be interested to know that, in fact, a purported chapter from the book, written by Mr. Smith, exists...
In chapter 62, Maka and Soul fight a murderer named Frey D.Sadoko, who makes her victims listen to a cursed recording before killing them in their nightmares. She also uses an attack called Nine Inch Nails.