This BBC Earth article
suggests possible real backgrounds for the lotus of lotus-eaters (Λωτοφάγοι), Cyclopes, moly, Scylla, Charybdis, and the cattle of Helios. I generally find it quite difficult to be truly convinced with these, but some of them might ring true. I do know that many mythological characters and myths themselves can be plausibly explained. I think, for instance, that we recently outlined Amazons’ background not totally unsuccessfully.