Okay, so I just read a very thought provoking post over at Farsight Blogger entitled "Cthulhu of the Rings in the Dark Ages of Middle-earth". The post is about using the Cthulhu: Dark Ages rules to run a Middle Earth game (and worth reading), but I was immediately struck by the possibilities of running a full-on mythos based Middle Earth game where Sauron is replaced by Cthulhu or one of the other Cthulhu mythos baddies. Replacing Sauron with Cthulhu means that certain other key elements need to be altered as well. So a light retouching of Middle Earth to make it mythos could include:
The Big Boss
As mentioned above, we replace Sauron with Cthulhu. Part of the Cthulhu mythos is that Cthulhu is imprisoned deep beneath the sea in R'lyeh. So for Middle Earth R'lyeh could be beneath the Sea of Nurnen in Mordor. The Sea of Nurnen looks on the map to be roughly 150 miles long by 50 miles wide. That's about the size of Lake Ontario or the Gulf of Finland and so reasonably large. Or you could put R'lyeh somewhere out in Belegaer, the Great Sea. Another is to have him somewhere under Numenor, making the revolt of Numenor against the Valar gods a Cthulhu cult uprising. Either way Cthulhu would have an insubstantial nightmarish avatar manifested in Barad Dur.
The Ring Wraiths
In the original, these were nine human kings seduced by the lure of power into taking the rings. Eventually the fell under Sauron's will through the rings and now serve even unto death. For a Cthulhu version you could keep the ring idea, but instead of becoming undead they become immortal mutants. They would look like D&D mind flayers: a repulsive humanoid body with the head and tentacled face of Cthulhu. Maybe with the vestigial wings as well.
In Tolkien, orcs are cruelly corrupted elves. The idea of elves (and humans) being taken and corrupted into a monstrous race fits perfectly with the overall mythos theme. But for a mythos version they probably shouldn't look like the stereotypical big green gobliny types like in Warhammer. So, you could make "orc" a general term for corrupted versions of the major races: svirfneblin (gnome), drow (elf), duergar (dwarf), derro (halfling), and grimlocks (human). That gives you some extra variety in "orcs" while working with the mythos corruption idea.