Fritz Lieber’s Nehwon Ghouls had translucent skin, so they looked very much like animate skeletons, I yoinked that for the orks in one of my homebrews, though each of the subspecies had different colored bones.
Were they still savage and barbaric? Of course! But there was almost no way to assign them any of the visual stereotypes associated with any of the RW peoples demonized and dismissed as being little more than upright animals.
I also used the small, bat-winged, 8-eyed Seshayans from Alternity: Star Drive as a replacement for Drow in another homebrew. Introduced as being deferential to others in the early campaign, it became revealed that they had once ruled the Underdark until being defeated in a massive war that scattered their people and reduced their cities to rubble AGES ago. Most Seshayans and surface-dwellers were unaware of that history, but then some Seshayans uncovered the truth...and hungered for a return to power...
Or as I posted in another thread, take your typical D&D high elf society and make them into xenophobic cannibals (like Athasian halflings).
Speaking of Athas, what about Thri-kreen? Too beefy? Tone them down a bit. Make them size small.
This isn’t rocket surgery. 
Besides the aforementioned Nehwon Ghouls from Fritz Lieber?
The Omec from
Defiance were a purple-skinned race that was so technologically superior to all the other alien species in the series that it took a multi-species alliance to defeat them. Why the animus? Because the Omec thought of “lesser” races as cattle and toys.
Stephen Donaldson's Amnion (The Gap novels) and Star Trek’s Borg come to mind. You probably know the latter; the former were similar, but used nano-level, gene-altering biotech for assimilation. Instead of looking like cyborgs, the Amnion resembled waxwork figures that had been too close to a heat source...sometimes with appendages in the wrong number or location.
Larry Niven’s Kzinti and Slavers? Different power levels; both fine for villainy.
The animal-men of H.G. Well’s
Island of Doctor Moreau?
The amphibious Deep One/human hybrids from HPL’s lore? (And him, a notorious racist!)
Daleks and Cybermen from Dr. Who? Yes, even those can work in D&D: they weren’t evil, but for one homebrew, I reskinned Eberron’s Warforgedas being psionic dwarves animating metallic bodies. Effectively Cybermen. making them evil takes a few words in the description.
(I could go on. I’m choosing to stop.)
Yes, they’re all over the pace in terms of formidability, but that’s just a matter of mechanical tweaking. The key is none are likely to be described in terms associated with RW bigotry.
