Can you recommend setting material for roleplaying games (books, websites, etc.) that presents places in the real world but with supernatural overtones based upon a locale's myths, fairytales, and legends?
GURPS Places of Mystery might be good for this. Despite being a GURPS book, it's not very system-specific at all. It's more oriented towards human constructions that have mythic overtones than towards completely natural places, though. I can't find any reviews other than the one I wrote a long time ago, here, which is oriented towards Feng Shui.
Ars Magica has a bunch of sourcebooks with mythic real world location.
King Arthur Pendragon for Arthurian Fantasy. LOADS of information, and really well done. Greg's a bit of a scholarly type, on top of it.
4th Ed has the most comprehensive rules; it's the only edition with magic available for PC's.
It also has a setting sourcebook for Beowulf era Scandinavia.
Robert Grave's "Poetry" being his Greek Myths and White Goddess advance a full mythic system (a modern poetic reinterpretation of various Greek stories), with the interesting side effect that all Male Heros Must Die.
Graves hypothesises that neo-lithic European culture shared a single cultural basis in a myth about a Mother Goddess and a Sacred Sacrificial King.
Graves hypothesises that this became myth as various tribes rejected the concept of sacrificial Kings. Graves claims that Kings were either half-year Kings, with the summer and winter Kings murdering each other; or that there was a singular King with his "inverse". Eventually Kings resisted being killed, using boy substitutes, "one day" adult male substitutes who die on the day they're made king, extending "King for a year" to three or seven years. Graves claims that Greek myths are reinterpretations of wall cartoons of the actual myth, and that a singular mother goddess is reread as a sequence of repressed various female goddesses.
Graves links this with the ages of man, and ideas about pre-agricultural and agricultural myths—these concepts are often used (via Tolkien) for the generation of fantasy races. So Graves' myths are compatible to the standard fantasy world via this method, or via the "multiple ages of the world, multiple races" system.
Graves is batshit insane, but his mythology is more detailed that Lovecrafts, and just as creepy when it comes to burning children alive because the King doesn't want to stop being a King.
Just a few off the top of my head:
Qin has a lot about China before the Empire. Exceptionally good.
Tibet has a lot about, not a shock, Tibet. Exceptionally good.
Hoodoo Blues has a lot about Voodoo.
Northern Crown is set in "a colonial New World where the legends of North America come alive".
The Palladium system has a number of sourcebooks for various implementations of their "meta" roleplaying system, include such books as "Mystic China" (Ninjas and Superspies), and their Rifts system had a number of books for real-world settings that fit into the SF/Fantasy setting from which you could pick and choose elements.