Yeah, these two phrases are joined at the hip for me!
NDT was better the second time around, I'll give it that; but by 'better' I mean it went from abysmal up to merely below average.
I've been wondering about that.
The best use I could see for it now is to be the core region of a campaign that starts there; all the little mini-adventures within NDT get fleshed out into something a bit more significant (e.g. "Expedition to the Ruins of Xitaqa" could easily become its own complete adventure) and the campaign rattles around in there for ages.
That's more or less what I've done with it. And mixed in Thunderspire Labyrinth, Speaker in Dreams, Heathen (a 4e Dungeon adventure that should have been on my list) and a few smaller vignettes.
I used Minotaurs as the ancient race (fits with Thunderspire Labyrinth), used bits of Thunderspire Labyrinth plus the dungeon with the gelatinous cubes for Xitaqaa, and used Heathen for the contents of the lost valley.
As for the main topic: those modules you listed as being good, what in your view made them good?
For the WotC adventures I think I listed this.
The Giants I enjoyed at the time (25+ years ago now) just for the sheer dice rolling, giant slaying insanity of it. I am looking at converting G2 to 4e and sticking it in the Feywild, but will certainly be toning down the combat a bit compared to the original.
Castle Amber is light-hearted fun. I wouldn't use it in a serious campaign, I don't think. It was good for a two-or-three session 3E experiment. (As I said, the module was more fun than the system.)
Descent Into the Depths has nice stuff with factions. When I ran it (in Rolemaster) the party included a dwarf who couldn't speak Common, and the only other PC who could speak Dwarven was the party elf. Who was therefore negotiating between the rest of the group and the dwarf PC. And also negotiating between the whole group and the drow. And that elf PC was himself a sociopathic worshipper of Demogorgon. Naturally enough, hilarity ensued. Until the PCs got badly hurt in a fight with some mindflayers who they were trying to clear out so as to get in good with the drow. I can't remember exactly what happened with the troglodytes, but I think there was some sneaking past them, and I have vague memories that some of the PCs at least got captured by them. I can't remember now how they escaped.
Night's Dark Terror I like for its tropes: goblins laying siege to the homesteads, wandering through the forest, fey islands, shadow tombs, gnoll marauders, etc. As written it doesn't have a lot of thematic depth, but those fantasy tropes made that depth easy to introduce: rescuing prisoners; revenge against goblins; defeating Bane-ite, Orcus and Vecna cultists; etc. It actually mixed very nicely with Thunderspire Labyrinth (I merged the characters of Paldemar and Golthar - Golthar was the evil wizard's name in Goblin, Paldemar when dealing with humans - and I built on the Thunderspire Labyrinth idea of him being a Vecna cultists).
Finally, the two Oriental Modules I ran (and I remember now I've also used bits of a 3rd, OA5 Mad Monkey vs Dragon Claw, in the same campaign) are also excellent for tropes that easily support thematic stuff. OA3 is all about going to an island to defend against the spirit warrior haunting a trading colony, and getting dragged into a bigger struggle taking place in the spirit world between spirits of nature and an undead spirit. OA7 has similar themes of immortality in conflict with nature - a dragon who was once an animal lord, but got demoted for bad behaviour, is trying to gain immortality by learning techniques to breathe a special substance which, when it replaces the ordinary atmosphere, will be fatal to all other living beings. (Naturally, I linked the necromancy in OA7 to the necromancy in OA3, creating a bigger conspiracy/campaign background.)
So as well as all the cool tropes of spirits, snake cults (worshipping the dragon in OA7), the Celestial Bureaucracy, etc, I was able to bring out ideas about duty, betrayal, loyalty, passion etc. This was the same campaign that also went on to use Freeport and then Bastion of Broken Souls to mix in ideas of freedom, transcendence, karma etc. A very satisfying campaign, even by the end of it I swore an oath never to GM Rolemaster again (it's way too much work to make it work, especially at high levels).