Darker and Edgier: Akamatsu-sensei appears to be rapidly accelerating his use of this trope. Chapters 277 and 278 feature Rakan and a boatload of Mauve Shirts being dissolved into flower petals, and the dozen-odd chapters before it feature an ominous secret that borders on Go Mad from the Revelation, the story of someone who saved the world being sentenced to a brutal death for it, and Negi nearly murdering the wrong person for revenge.
Darkest Hour: Well, see above. Most of what happened after the Governor's ball trumps their previous predicament in awfulness.
To see how bad it's gotten since then, see Total Party Kill. It doesn't get much darker an hour than that.
Dark Is Not Evil: Varies, but the few right bastards have all been humans with no explicit connection to darkness.
Also, Kagetarou, who looks like a villain at first but turns out to be Jack Rakan's buddy. Now we have a shadow-user named Dynamis in Fate's group, and this new guy is quite evil, erasing people from existence and making it quite clear that he intends to kill Nodoka, even using her as a shield and coming close to snapping her neck before Setsuna saves her by hacking off his right handnote He seems to believe that he's doing them a favor by killing them. Then there's the whole summoning shadow demons thing he does, including a huge one.
The demons showcased so far have all been perfectly amicable, at worst neutral characters who just happened to be hired by the enemy team and don't seem very pleased at having to cause serious damage. Justified in that the "Demons" are a race of the Magical World. The more demonic looking ones are a different kind of demons. The demons summoned in the Kyoto arc are oni. Setsuna and Kotarou are half-Youkai (Han'you). Demons like Mana and Poyo are a different kind as well.
Magia Erebea is... pushing it. It is not explicitly evil, but not the kind of power expected from a paragon of virtue either.
Dawson Casting: Most people in the Live Action Adaptation seem far from their supposed age
Day in the Limelight: Almost every girl gets a chapter, or even an entire arc, devoted to her. Especially if she hasn't had much "screen time" yet.
Lampshaded when Negi (in his bishonen form) tells Ako that `everyone's the main character in their own life'.
Defeat Means Friendship: Mostly subverted (in that the people fighting are already friends, and are in a tournament or whatnot), but played straight with Kotaro and Eva, to a lesser extent.
Recently Negi declared he wants to become Fate's friend. Given the characters you can guess how this "befriending" is going to happen.
Defecting for Love: Given some developments involving Negi inadvertently romancing one of Fate's most trusted subordinates out of her disguise against her will and creating a pactio with her at the same time. Add the fact that her perfect disguise seems to drop only during times of intense emotion felt on her part, such as love, and it's as good as done.
Deliberate Values Dissonance: Slavery is a state-sanctioned practice and completely normal in Mundus Magicus. Seeing how they use Latin as (one of) their main language and that the political powers date back to Middle Ages if not Ancient Rome, this is to be expected. The current slave system was created by Queen Arika to deal with the thousands of Ostia's homeless after the destruction of their country. Slaves can buy their freedom and are protected against "excessive mistreatment", which the Slave Collar reports automatically, but the electrifying feature of the Slave Collar doesn't seem to fall under "excessive mistreatment" until the heroes beat the the crap beat out of a guy who did it and told him that he was going too far. There might have also been other, off-screen punishments, it was explicitly stated that it's only supposed to be used if a slave revolts or a similar extreme scenario scenario.
Departure Means Death: Magic World natives cannot survive on Earth, so when the magic world goes they'll go with it. Albireo may be an exception, but he might just be a book instead.
Designated Girl Fight: Odd gender inversion: despite the series having far more women than men, the majority of Negi's opponents have been male. At this point, the only named male characters he hasn't fought are Eishun, Johnny, Filius Zect and some of the magic teachers.
Despair Event Horizon: When Asuna dies in Negima!, Negi splinters like a broken broomstick. His artificial cheerfulness masks it temporarily, but it quickly becomes ghastly.
In the original manga, Negi probably crosses this after Fate attacks his students at the Gateport and scatters them across Mundus Magicus. It isn't quite as bad as in the anime, but the fact that he was completely unable to protect them after he promised to do so really gives him issues later on.
Played for laughs after Rakan's hilarious first failed attempt to teach Negi Magia Erebea. "I'M GONNA DIE."
Rakan MADE this happen, purposely depressing the crap out of negi after his "Make a bad face and punch!" initial plan doesn't work. Also those were meant to be strong punches, Rakan told him to do 1000, which even for normal people would be quite tiring.
In the manga, this artifact has a completely different purpose and gets explained in detail. But in the anime it's an Ass Pull that's immediately used to solve what had been an apparentlyunsolvableproblem.
During the Magic World's final battles, a much more literal example: when Quartum pulls out his final move, EnteiShoukan, Negi jumps out with Raisoku Shundou and literally socks it across the face!
Dirty Business: Negi wonders if defeating Chao's plan to reveal The Masquerade was the right thing to do throughout the Festival Arc. He's reassured by Chao herself, no less that there are no hard feelings, though.
Double Standard: Abuse, Female on Male: While this doesn't occur much (likely due to the fact that Negi is only ten), in one story arc where Negi gets aged up to 15, he suffers a few smacks in the face. Anya, his best friend from home, is also able to beat him up as much as she wants since they're the same age.
Downer Ending: The character arc of Chisame Hagegawa goes through a long period of her growing accustomed to magical shenanigans and finding that she enjoys them but in the epilogue she's a hikikomori that rarely even sees Negi or the rest, dropping her back into the life she once had but no longer able to enjoy it.
Eldritch Abomination: Two so far: the demon that Evangeline curb-stomped in the Kyoto Arc, and the huge black shadow-demon summoned by Fate Averruncus' shadow-using minion in the Ch. 270's.
Appropriately, this one also gets curb-stomped, this one by Chachamaru's Kill Sat Artifact.
Elemental Baggage: Subverted in the literal sense, but invoked by Evangeline and Chao's high-level elemental spells. The supplementary materials at the back of the tankobon explain that Kosmic Katastrophe breaks the Laws of Thermodynamics, and that freeze spells are considered higher-level than fire spells because they break more laws.
Elopement: Nagi suggested to do this with Princess Arika when he realized she had developed feelings for him, getting a blast of magic in response. Ironically, they end up eloping after he rescues her from her execution.
Evil Chancellor: A group of them has been manipulating the Megalomesembria Senate and is responsible for every major event that has happened in the story so far, starting with the war. Even the events of the Festival Arc may have been a result of their actions.
A few of the girls are based off of the characters from Love Hina: Naru (Asuna and Chisame), Shinobu (Nodoka), Kaolla Su (Ku Fei), Motoko (Setsuna, Akira and possibly Madoka), Kitsune (Asakura) and Mutsumi (Chizuru).
Fan Disservice: There's a surprising amount of Squick in the series, since many fight scenes against severelymessed-uppeople occur with the girls in various states of undress. There's also guys in states of undress.
And more than one Fanservice Extra: Check out the girl in the lower left panel of this page. She encapsulates about 12 different Turn On Tropes and adds nothing whatsoever to the story except some eye candy.
Fantastic Arousal: Setsuna's wings seem to be very sensitive, and poor Chachamaru can't seem to impress on Negi to wind her up slowly and gently.
Her own damn fault in that she keeps telling him that it feels good and Negi, being only ten, thinks that more is naturally better. Chachamaru ends up talking in a wingdings-like font from the overwhelming pleasure.
Fantastic Racism: Against woodnymphs and other demihumans by humans, who also had no problem cutting horns off them(a bit like real life, the horns, not hunting humans) and selling young girls into slavery.
First Kiss: A lot of the girls on Negi's team have their's with him. Negi himself gave his to Asuna and her's to him.
Almost every person acts very nervous as well, and then came Asakura's turn. Her pactio was the only one to occur off-screen and she was so not nervous about it that she got a commemorative photo for it.
First Name Basis: In a similar vein, Konoka spends most of her time trying to get Setsuna to call her 'Kono-chan' rather than 'Ojou-sama'. It doesn't work.
Flash Back: Sayo's memories in episode 19, Konoka's in episode 21. In the manga, Asuna also gets many flashbacks related to her mysterious past with Ala Rubra.
The most hilarious take on this trope is when Rakan watches Homura's Flash Back.
A lot of Asuna's abilities and fractured memories are a hint as to her true nature, especially her magic cancel.
The location of the Magic World is suspiciously never mentioned. When the series actually gets to it, we get a few pieces of information from time to time that help point out where it must be. Most importantly, we're given the size of the place (slightly less than one third that of Earth) and the location of features such as Olympus Mons.
Forgotten Phlebotinum: The Pactio cards ability to summon the partner to the master, no matter where they are. You'd think that would ruin the kidnapping plot in the Magical World Arc quite nicely.
For Science!: Hakase's justification for peeking into Chachamaru's 'treasured images' folder. Never mind that this effectively meant probing Chachamaru's mind against her will, on the subject of her crush, no less.
Freudian Excuse: Played with in Eva's case: after recounting the tale of her life, including how she became a vampire and killed her way through the centuries, Asuna's response is immediately "So... it's not your fault, right? Because you didn't choose to be bad?" Eva takes this as more evidence that Asuna is an idiot.
Friend or Idol Decision: The end of "The Great Baka Rangers and the Secret Library Island Final Exam Operation" arc.
Fugitive Arc: Negi and company go on the lam during the magic world arc.
Full-Frontal Assault: Dynamis, of all people, does this in the final battle. No one saw it coming and no one knows why he did that... (though Takane D. Goodman mentioned earlier that her Shadow-created clothes provide even higher defense with direct skin contact, and Dynamis does use Shadow magic)
Full Moon Silhouette: Near the end of the Kyoto Arc, after Setsuna rescues Konoka from the clutches of the enemy.
Eva has one at the beginning of the Mahora Blackout Operation.
Fun Size: Both Sayo and Setsuna have an absolutely adorable smaller form. Then there's Chachazero, who despite being psychotic can be quite cute.
Functional Magic: Most of the big spells will have enough explanation in-story for the reader to really get a feel as to what's going on and how it works. The appendices in the books give properly scientific and historical explanations for the spells, leaving enough room in the physics for the "it's magic" kind of Willing Suspension of Disbelief. This goes to create a very real-feeling system of magic that creates a link between ancient beliefs and modern scientific understanding, helping to tie the world together as "our world, but with magic".
Furo Scene: Quite a few, starting with a furo the size of a swimming pool.