TNE isn't automatically darker IMHO, although I tend to slant it that way myself. The old Imperium offered very many opportunites for horror, just what *is* on all those many interdicted worlds? The New Era does lend itself more towards new hope and optimism, after the horrors of the Black War and Hard Times. I tend to go for the hope/disappointment contrast that seems to abound in TNE. I deepen the disappointment troughs towards the fourth act of the story arc, and then hit home with something stark at the climax, with the players snatching optimism out of the jaws of horror 50% of the time, and emerging with dignity, wiser but with less sanity the rest of the time.
What's been interesting for me is how my players reacted to TNE - in all our classic Traveller games, no matter how much I saddled them with dependents and loved ones and reasons to come home, they felt no ties to home and ranged far and wide through the universe. As soon as we started playing TNE and I got the feel of the New Era across to them, they kept going home to check that their wives and kids were safe. From feedback, they seemed to feel that the RC was a much more coherent universe.
Anyway, I used their newly found sentiment to great effect by threatening their families in a drug-fuelled crime wave on their homeworld, and by endangering their headstrong kids who tried to run away from home and conquer the stars like mum & dad, by stowing away on merchant ships. Needless to say one of the kids died and another is still held hostage out in the Wilds.... I guess if I was really chasing the horror angle I'd have really nasty stuff happen, but I prefer to tug at the players' heartstrings more gently....
I think the horrific things that are out there in the Wilds are mainly a lot of basic things that were previously eradicated or kept under control by the old Imperium.
Disease is the biggie IMTU, with lots of new nasty diseases running rampant and unchecked through many of the planetary systems. IMTU there was a LOT of biological warfare during the Black War. My PCs have been quarantined quite a lot on their way back from expeditions (sort of Final Fantasy: The Spirits Within kind of feel to it).
Religion is the next one - despite my own faith I recognise that more people on Earth are killed in the name of religion than for anything else, so I have transferred that to my TU. Loads of religions have sprung up in reaction to the Hard Times and Long Night, and I have managed to get even my players suspicious of certain high tech devices (they just can't shake the boogieman stories they were told as kids about Black Globes, Lucanian technoology, etc).
Avaricious self-interest is the next. I'll cite the bad guy from FF:TSW as a good example. M TU has psychotic robot inventors, deluded scientists, ill-advised politicians, harmful supposedly 'helpful' genetic modified crops, etc.
I began my campaign with all this endemic in the RC, and when the players got out there into the Wilds it was all there times ten.
Individual horrors have been:
the discovery of the planet-wide practice of wiring disobedient citizens into machines that torture them for the rest of their lives;
the child-labourers of the planet moon who are worked to death so their parents can live in luxury;
the botched cloning experiments of the science community on a paradise planet in the Wilds;
a planet whose ruling military elite experiment with germs and chemicals on their own troops in battle;
the tragic artificial lifeforms of former high-tech planets who have lived through the dark times thinking they were human until they met the PCs from the RC and suffered critical culture shock that destroyed their stable society (nice one Star Vikings
);
planets where the arrival of the PCs brought germs that wiped out the un-immunised planetary population within months of arrival (that adventure was the subject of a cover-up and war crimes trial back on Aubaine);
etc
All my horrors are human-based, it seems to hit my players harder that way, than say an old doomsday device etc. When they have to go to a boneyard world I always make sure they encounter the real lies that once lived there. It helps that one of my PCs is a remnant, and that player is very good at playing the distraught melancholy that comes from being part of the civilisation that caused all this destruction.