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: Yoshi. He manipulates everybody to fight everybody, kills people in a very cold manner and his motives are unclear till the midpoint of the series - he says that he is trying to "create" a new strong leader, if this can be considered an excuse. What's worse is that you think that this is the worst things can get, until Kano comes along. This being the man who would be an Omnicidal Maniac if he didn't have so much fun playing with human beings and turning them into abominations of nature, and then discarding them as soon as he gets bored of his new playthings. He thinks it's funny!
"Code 07TX", the main action theme of the series is also rather awesome and gets played over several intense action sequences such as the giant Kill 'em All shootout between Onishi and Tsuginaka's respective Organo branches.
The series is kind of about this trope. Nothing the characters do has any hope of saving the world, as it turns out; and there are copious hints that this is the case; but the series is very tight-lipped about it, and up to the moment they turn into plants, it looks like the Shapes (that is, the bad guys) might have lives worth living. And we don't get confirmation of Ran's death until the last few minutes. So the first viewing becomes a sort of staring contest: How much do you care about these characters, and how much hopelessness are they worth to you?
Everyone Is Jesus in Purgatory: Inevitable in a series this abstract. One theory among fandom holds that Kano is telling the truth when he claims that Lux exists only within his mind.
By the end, the series is so heavily saturated in Gnostic symbolism and ideology that you can hardly move for the paranoia, philosophical debate (or maybe "dog fight" would be a better word), and archetypal parallels. The fact that Kano actually thinks he's the demiurge does not help things.
Wait... wouldn't that make Doc Sophia? Embodying gnosis in the material world through texhnolysation? On second thought...
Magnificent Bastard: there are a couple running around. The most prevalent is Yoshii, who, well, outright manipulated all the factions in Lux against each other, but with so many paranoid people running their own highly convoluted agendas, a good chunk of the cast qualify for Manipulative Bastard in the very least.
Probably one of the most disturbing moments is when we get a glimpse into the process of making one of the Shapes. He just keeps smiling...
The Shapes show up again as a source of Nightmare Fuel at the end: they have grown strange metallic roots out of their feet, and they still keep smiling. Except their faces keep spasming every few seconds into what can only be described as sheer pain and horror.
It's probably not pain - they've just lost all muscle control, and most don't even seem to be conscious, any more.
Kano himself probably qualifies as Nightmare Fuel. Well, at least his mind does.
Ichise getting one of his legs and arms cut off in retaliation for having used his fists against a woman who stuck her nail in his eye during sex.