Ctulhu works great with Traveller imo especially as a lot of the Old Ones are psionic aliens and the Droyne are almost Mi-Go already.
The whole Droyne/Ancients trope is great for a Lovecraftian twist. The idea that Grandfather spread humaniti across the universe, and tinkered with many of the races, means he very likely gave whatever boost humaniti needed to become a technological species. You have ancient ruins, pre-humans to worship and/or slave for alien beings, psionics and practically magical technology. All the elements of a great horror campaign.
One standard Lovecraftian theme is "the more you know the worst off you are", or that study leads to madness. Books that can drive a person mad, or alien "gods" whose very presence on a world can drive humans insane - these sound like psionics to me. The knowledge in a book can't really drive a person insane, not in a reasonably standard SF setting, but some sort of psionic artifact can. I can picture an archeological expedition to Ancient ruins that can ultimately activate such a device, maybe even some sort of android, that is tuned to droyne mental frequencies that drive humans insane.
From a player point of view the more successful the dig is, the worse off the players are. They can be tasked with investigating and trying to stop the disturbances, or be part of the team on the dig, challenged with figuring out they have to stop their boss from completing the research.
Another Lovecraftian trope is fear of what you will find in your family tree, and inbreeding. This brings to mind lost colonies, probably with genetic engineering, that have horrifically failed, or just some sort of genetic lab with questionable experiments. Related, and more "cosmic" could be research into Vilani and Solomani genetics that end up revealing what could be viewed as horrible things - like hidden shortcuts to ensure hominid control and the like that the Ancients implanted.
The Droyne, and especially Chirpers, as the degenerate offspring of the vastly superior Ancients is a great Lovecraft call-out.
Any number of classic movies and books could be mined for Lovecraftian influences on SF, and therefore translatable to Traveller. The Alien movies, The Thing (either the old 50s version or the John Carpenter remake). One of my favorites is Larry Niven's
World of Ptavvs. It has everything Lovecraftian - ancient statues, research, madness, a tentacle faced monster, cosmic horror of human origins, exploding planets - OK, that last isn't so much Lovecraft. Its pretty famous, at least for someone my age, so a GM might have a hard time passing it off on his players. Then again just replace Kansas City with a Zhodani world, Kzanol with an Ancient and you're on your way.