I can't remember if Lord of the Rings was in the original appendix
It was. But not capitalised. (Gygax capitalised the biggest influences.)
Do you have a quote where he says he didn't like it?
From Dragon 95 (1985, p 12):
Though I thoroughly enjoyed The Hobbit, I found the “Ring Trilogy” . . . well, tedious. The action dragged, and it smacked of an allegory of the struggle of the little common working folk of England against the threat of Hitler'’s Nazi evil. At the risk of incurring the wrath of the Professor'’s dedicated readers, I must say that I was so bored with his tomes that I took nearly three weeks to finish them.
"Tedious", "dragg[ing]", "bored" - that's a pretty unequivocal indication of dislike.
Some more highlights from the same essay (which include some words of praise):
Considered in the light of fantasy action adventure, Tolkien is not dynamic. . . .
The wicked Sauron is poorly developed, virtually depersonalized . . .
"“Ent"” is interesting; Tolkien took the name from an old Anglo-Saxon word for "“giant",” and his treatment of them as sentient trees is inspired. This sort of creature appears in both game systems. “"Orc"” (from Orcus) is another term for an ogre or ogrelike creature. Being useful fodder for the ranks of bad guys, monsters similar to Tolkien’s orcs are also in both games. Trolls, however, are not identified well by the Professor . . .
Gygax then goes on to explain how elves and dwarves in D&D are derived from the same mythic/fairy-tale sources as Tolkien drew upon, rather than from Tolkien himself.
Tolkien was a great artist of the imagination whose sub-creation was so vividly envisioned and finely wrought and balanced
<snip>
Tolkien had his own unique, and truly exquisite, vision of this "mythopoeia" which has proven to be the most influential in the history of modern fantasy literature
<snip>
The best of post-Tolkien fantasy taps into the same archetypal depths and may even include elves, dwarves and orcs--or some variation on those themes--but crafts them into new, unique forms. It is too bad that most fantasy authors and RPG designers focus mainly on secondary influences, which ends up leading to derivative sub-creations.
Dark Sun was definitely one of the bright points in the creative history of D&D. I too would like to see more variants on the core tropes. On the other hand, I'd also like to see WotC try to present a classic setting with a fresh look.
For me, at least, what distinguishes Tolkien from a lot of D&D fantasy is that the presentation of the world - however imaginative - isn't an end in itself. Furthermore, the presentation of the world is disciplined by acknowledged external constraints, against which the accomplishment can therefore be measured.
Two examples, from Tolkien, to illustrate what I have in mind. First, Lothlorien: in terms of "external constraint", this is an attempt to make the "fairy wood" trope believable within the context of the (largely naturalistic, though not particularly modernist) contemporary novel; but it serves a larger purpose, of creating the narrative space in which the tale of Galadriel's redemption can be played out.
Second, the Undying Lands: in terms of "external constraint", this is an attempt to present a coherent, novelistic treatment of the "land to the west" that is part of British/Celtic mythology; but it serves a larger purpose, too, of enabling a distinctive (and non-Christian, though recognisably informed by elements of Christian ideals and literature) retelling of the fall, and of the possibility of salvation.
The only treatment of classic north-western European fantasy material that tries something comparable to this, that I can think of, is Wagner - also on redemptive themes, although of a much more modernist and 19th-century-revolutionary character than Tolkien.
A D&D world like Dark Sun seems to me to suffer in comparison to these sorts of works. The tropes are novel, but they don't seem to be achievements in either of the dimensions that I've described above for Tolkien's work. Though REH has obvious weaknesses as a writer (but doesn't Tolkien too?), I think his Conan stories are more interesting for the general sand-and-sandals genre than Dark Sun. I personally wouldn't put him on the same level as Tolkien (no doubt others would disagree, including probably Gygax), but he does discipline existing tropes drawn from historical and pseudo-historical fiction, and at his best put them to work for a larger thematic purpose (ultra-modernist and somewhat nihilistic, in my view, but that's not, or needn't be, a criticism).