Accidental Pervert: Poor, poor Kouta-kun... no matter which story he's in, he still gets hit with this trope hard. Gohan to a lesser extent as well.
Adaptation Expansion: The series has added some to the Unknown Man, stating that he's Kakuzawa's nephew (fans did speculate in canon that they were related, but the series never said anything about it), and that he used to work as a hitman.
Apocalypse How: Gohan and Goten end up on the same beach where Kouta and Yuka first encounter Lucy as adults. Early on, nothing is directly stated about what happened to the AU Dragonball-verse they came from, except that it cannot be returned to. But when one considers the galactic scope of the people Gohan's friends and family knew, the fact that they fled the universe entirely places what might have happened somewhere in the Class X: Planetary Annihilation to Class X-4: Universal Destruction ranges.
Black Comedy Rape: Nyuu does this in a few different chapters. While her sexual harassment of other characters is always treated fairly seriously, the situations involved are so over the top that it's hard for the viewer not to laugh.
Blood Knight: Gohan's Split Personalities, Oniari and Makai. The slipelit Juuichi actually breaks out of her holding cell, just so that she can test her ever increasing combat abilities against the research facility's security. It's even outright stated that it wasn't the first time she'd done so either. And of course, Bando.
Played straight and deconstructed with Gohan. In comparison with the original series, he actually does get broken over his traumatic childhood experiences. This eventually leads to Gohan making several mistakes that result in the deaths of his friends, most of his family and the destruction of his homeworld. It effects Gohan immensely at the start of the story and causes him to be highly critical and over jugdemental of his actions. After moving into Maple House, he slowly starts to get better.
Inverted with Nana. Despite her harsh life in the facility, she is probably the most optimistic girl you'll ever meet.
Inverted with Juuichi. Instead of breaking under the facilities experiments, she grows stronger, both physically and mentally, to the point of developing a cocky and haughty personality that takes great pride in not only having survived, but even thrived in the harsh evironment.
Chick Magnet: To Gohan's confusion/embarrassment, he gets more fangirls after he's seen wearing only a pair of swim trunks at the school pool.
Clingy Jealous Girl: Yuka and Lucy, just like in the original material, show this in spades towards Kouta. Thanks to helping her come to terms with the rape she suffered at the hands of her stepfather, Mayu becomes some variation of this trope towards Gohan. This is justified by him being the only man, or any person really, that she has complete trust in. Nana too, to a lesser degree, and also towards Gohan.
Curb-Stomp Battle: Gohan has, so far, won every battle he's fought in without putting any real effort into it.
Darker and Edgier: Some of the stories scenes are more explicit than the canon material. One notable instance is Mayu being raped by her stepfather. The scene is described in great detail.
Death Glare: Lucy gives a particularly frightening one, mainly because death soon follows, making this a literal Death Glare.
Genre Savvy: Gohan has managed to be this, figuring out Nyuu and Lucy are split personalities due to himself being in a similar situation.
Groin Attack: Gohan incinerates Mayu's stepfathers genitals as punishment for raping her.
Healing Factor: Within hours after beating up Lucy, Gohan sees most of the wounds healing across Nyuu's naked body...
Healing Hands: Apparently, Gohan got Dende to teach him a thing or two. He notes that he's nowhere nearly as good as Dende, since it takes longer for him to heal non-lethal than it does Dende to heal near fatal ones.
Immune to Bullets: Gohan, as some unfortunate SAT operatives find out. Also, the Diclonii can use their vectors to block bullets, though they are rendered useless against heavier rounds such as shotguns and anti-tank missiles.
Innocent Fanservice Girl: In this version, Nana is one (though she in canon she didn't have problems walking around naked either). Nyuu is still one as well.
Ki Attacks: It IS a DBZ crossover fanfic. What did you expect?
No One Could Survive That: Lucy assumes Gohan couldn't survive being buried under a pile of tombstones after she pummeled him. Gohan is quick to prove her wrong in classic Dragon Ball Z fashion. He even lampshades that an attack like that is nothing to him.
No Sell: Gohan does this to everything characters in this series throw at him. Lucy even pushes harder and lets loose four addition vectors against him with far greater strength than what she had before. This does nothing.
Only Sane Man: Yuka, just like in canon, is the only mentally stable and normal person in a house full of oddballs, though her jealousy for Kouta tends to get the best of her at times.
Oh Crap: Lucy's reaction(s) to Gohan during their fight when she finds she can't hurt him.
Person of Mass Destruction: Several, actually. First we have the Saiyans, who can literally blow up the planet with minimal ease, and then we have the Diclonii, who spread their genes via infecting human males and plan to replace humanity with a new race of people.
Puppy-Dog Eyes: Gohan proves why this is such an effective trope in chapter 6.
Rape as Drama: Mayu gets hit with this even harder than the original canon material. It's one of the few well written examples in fanfics and also serves as a plot point of Mayu building trust with Gohan.
Redshirt Army: Heavily armored soldiers with machine guns, who would normally be very effective against other human armies, tend to fall into this category when facing a Diclonius or one of the Saiyans.
Shout-Out: To some jokes in Dragon Ball Z Abridged, with Goten calling Gohan a nerd and saying that Piccolo called him that, and the one when one of Gohan's female classmates is asking him out, he says "I need an adult." Another made to Hellsing about hiring mercenaries with questionable backgrounds, with Hellsing being depicted as a Show Within a Show.
Shown Their Work: The writer claims this, saying he studies on actual rape victims before having the scene where Mayu is raped.
Superpowered Evil Side: Asides from Lucy being this to Nyuu, as well the DNA voice apparently inherent in all Diclonii we have the shocking example of Gohan having not one, but two of these: Oniari (Essentially embodying what Gohan becomes when he goes Super Saiyan 2) and Makai, who crosses straight into Enemy Within.
Twice Told Tale: Despite Gohan and Goten's presence, the story is recognizably that of Elfen Lied; they don't so much divert the flow as become part of it, and even the divergences keep it within what any EL fan would know; for example, when Kouta allows Professor Kakuzawa to take Nyu, Mayu still questions the Professor's story, while Gohan is outright furious with Kouta - as he might be with a certain also-gullible deceased father.
Though as an interesting note, the story has used bits from both the manga and the anime, though so far it things from the anime have been limited to moments of Nyuu groping, Lilium and the Music Box (now used with, and not as replacement for, Nozomi).
World Domination: Kakuzawa's eventual plan. How it differs from canon remains to be seen...