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.
Canon Sue: Lúthien. She has all the classic elements of this (great power, incredibly beautiful, Rebellious Princess, accomplishes a deed no one else ever managed, idealized representation of a real person, etc.), but Tolkien makes it work. The book's mythical style is probably why. Old stories are riddled with larger than life figures that cultures associate themselves with. Lúthien comes as this, and it is pretty clear the stories are painting her as some sort of great example of how to behave. It also helps that she's partly based on Tolkien's adored wife.
Cargo Ship: Fëanor loves those Silmarils more than anything. So does everyone else apparently, even Morgoth.
Melkor, later known as Morgoth Bauglir, begins life as one of the Valar, but his spite and arrogance precipitates his steady downfall into evil. Melkor begins by destroying the great lamps of Valinor and creating the pits of Utumno, where he takes as many races as he can and personally enacts hideous, unspeakable tortures upon them until all that remains are grotesque perversions that he can use as his servants, ruined terrible forms of life. After his first defeat, Morgoth repays mercy with treachery. He proceeds to destroy the world trees, betrays and kills the king of the Noldor elves and steals their treasures from petty greed, leading to the deaths of many thousands of elves when they pursue him. Once he sets up his base of operations in Middle-Earth, Morgoth gets back to his old business. He delights in corrupting men into darkness, manufacturing and playing off corruption in their hearts to set them against each other and their allies. His "crowning achievement" is tricking and beguiling the first men into swearing an oath of eternal fealty to him, meant to enslave the race forever in body and spirit, which is the reason why mortality is considered a gift for Man (souls of Men leave Arda and Morgoth's grasp). Morgoth launches brutal campaigns of slavery and genocide, with just one of the examples being the destruction of Gondolin, the most beautiful and proud elven city, with full orders to exterminate civilians, who are saved solely by the heroism of the city's warriors. Regions cease to exist with their inhabitants enslaved, wiped out or taken for horrible deaths. Morgoth also tries to rape the elven princess Luthien out of nothing more than cruel lust. Morgoth ends with no redeeming features whatsoever. An evil god, genocidal conqueror, brutal overlord, corrupter, Morgoth fits it all. At one point, he condemns a man to horrible torture and then enacts a curse to see his children grow, suffer horribly and be rejected by both life and death, solely because the man dared to defy him. There is no act too evil or petty for Morgoth. He commits atrocities on the petty personal and the grand, worldly scale alike.
Morgoth's Bastard Understudy Sauron is a demonstration of how those who were once noble can fall to great evil. Sauron was once noble Maiar who was swayed to Morgoth's side. Over time, Sauron's noble intentions for the world were replaced with vanity and lust for power. In the First Age, Sauron convinced a man to betray his comrades, showing him a vision of his beloved wife...once the man did what Sauron asked, Sauron revealed she was already dead and had his hapless pawn tortured to death as he had promised to reunite them. Upon capturing the hero Beren and his companions, Sauron placed them in his dungeons where he allowed his werewolves to slowly pick the group off, one by one, to torment the survivors. After the defeat of his master, Sauron fled to Numenor, assuming the fair form of Annatar, the Bringer of Gifts and seduced Numenor towards darkness and evil until it was a Morgoth-worshipping theocracy that practiced human sacrifice. This was an act so unholy, Eru Illuvatar, the equivalent of God, stepped in to destroy Numenor. Even then, Sauron was not done, and tricked the other races with the Rings of Power, forging his master ring to enslave all that lived. In the Third age, he embarked on a genocidal war for conquest, seeking only to feed his lust for domination and megalomania.
Darkness-Induced Audience Apathy: The Silmarillion, in fleshing out the history of Middle-Earth, paints the picture of a world which is an irreparably broken shadow of its former glory that will continue to backslide until a Ragnarok-alike event in the far future. It's understandable if this colours your enjoyment of The Hobbit and The Lord of the Rings somewhat.
More specifically, isolated stories/events in the overall history of Arda (Tolkien's 'verse) have endings that vary between depressingly and pointlessly tragic to highly uplifting—but the overall pattern is unmistakable. In almost every way, things used to be SO much better than they are now, and even major victories are (in the big picture/long run) simply putting a (often temporary) end to a great evil that has already done tremendous, irreparable damage to the world and civilization. So when the pattern repeats itself, the world (and civilization in general) starts out in an increasingly worse state than before, and ends up even worse than that by the end of the arc. Nothing quite like seeing what an endless cycle of Pyyrhic Victories over a world's entire history does to it, eh?
Fëanor. So, so much. Possibly because (as Jerkass Woobie notes below) despite making things far worse, and being a total dick, he was also a Badass.
Maeglin gets it too, though not as much.
So does Morgoth. Apparently, he looks like The Woobie for some. There is even a major Russian fanfic, The Black Book Of Arda, that even was piratey published as a book, that retells Silm from Woobie!Melkor's viewpoint.
Readers will tirelessly insist the elves are completely incorruptible and all their wrong doing can be justified. Obviously their genocides, child killing, refugee butchering, and stealing the Petty Dwarves' land count for nothing. Those readers usually cite The Lord of the Rings more than The Silmarillion.
Ensemble Darkhorse: Nerdanel. The amount of fanfiction and fanart she has received is in no proportion to the very limited pagetime she has in the published Silmarillion.
Fëanor crosses it when he leads a shocking massacre of the Elves who dared refuse him use of their ships.
Morgoth crosses this in the eyes of the Elves when he kills Finwë and steals the Silmarils. The moment that hits home just how evil this guy is, though, has to be the cursing of Húrin's family. Túrin's life was just one tragedy after the other, ending with his suicide. This is made even worse when you realize that all the misery was really caused by nothing more than Morgoth's anger. Especially since Túrin wasn't even the one that provoked Morgoth; that honor goes to Túrin's dad. Túrin's miserable life is merely a decades-long torture inflicted on Húrin as punishment for his defiance.
The creation of the Orcs is described as "the vilest deed of Melkor" and it's hard to think of any way he could have been redeemed after that.
Never Live It Down: Isildur. He performed many great and heroic deeds in his life, not least saving the White Tree and defeating Sauron. Nevertheless the White Council (and real life Tolkien fans) remember him mainly as the man whose hubris allowed Sauron to survive, completely forgetting the good things he did before his Face-Heel Turn.
Older Than They Think: "Earendel" is an old Northern European name for a god or a star or something along those lines. It seems to be one of those words that stick in peoples' heads: names like Earendel/ Horwendill crop up in the oddest places - James Branch Cabell and John Fowles's The Magus, and such.
Selfish Evil: Melkor stole the Silmarils and kept them from Ungoliant out of raw irrational greed, despite the fact that they painfully scarred his hands and burned all things evil that touched them.
Squick: What no one seems to mention - and admittedly the incest is rather distracting - is that Túrin essentially marries a child in a woman's body. Yes, Niënor was fully grown, but the Niniel personality specifically had to be taught to speak and understand 'as to an infant', and is only a few years old at best.
Strawman Has a Point: Eöl, being one of the Dark Elves who chose to remain behind in Middle-Earth rather than sail West to the Valar, hated Fëanor and the Noldor who fled Valinor and invaded Middle-Earth, even going so far as to kill Elves of Eöl's kin. Thus he refuses to cooperate with Gondolin or the other Noldor states, and allies with the Dwarves and (presumably) the Green and other Dark Elves.
Jerkass Woobie: Fëanor, so much. He gets a lot of sympathy and apologetic fans for someone whose actions directly set in motion a series of events that led to so much suffering and death, including genocide and a world-shattering cataclysm. Possibly because, despite being an asshole, he was also a total badass.