I'll deal with xxxHOLiC first, because it's the one with which I'm most familiar. In his book Foster devotes extensive attention to Yanagita Kunio (1875-1962), the renowned folklorist and inventor of minzokugaku or folklore studies. Foster divides youkai into two components, the mysterious and the weird, and in his consideration of Yanagita he quotes the folklorist from a 1912 essay: "And so in the end, all we can say is that human beings themselves are indeed the most mysterious [fushigi] thing in the universe" (145). This is almost exactly what Ichihara Yuuko says in the prologue to xxxHOLiC, and what Watanuki says at the beginning of xxxHOLiC Rou: "Of all the living things in this world, people themselves are the most mysterious of all."
CLAMP's invocation of Yanagita becomes even more resonant in light of Foster's discussion of one of Yanagita's essays from 1917 called "Hitotsume-kouzo" (One-eyed Rascal). In this essay, Yanagita offers a theory about the prehistorical origins of a certain one-eyed youkai, proposing that in olden times members of the community marked out for sacrifice had an eye put out to denote their status, and though the custom died out the belief that, in Foster's phrase, "a one-eyed person could receive sacred intelligence from the deities remained" (146). The origins of Kitarou, in Mizuki Shigeru's manga, anime, movie and print media empire, having only one eye are immediately clear, and the fact that Watanuki in xxxHOLiC and Ginko in Mushishi have only one eye seems not only natural but almost overdetermined. If they didn't have one eye, it would be impossible to trust their insight into the otherworld. Indeed, Ginko actually resembles Kitarou strongly, not only in their lacking a left eye but in the floppy hair they use to disguise the lack.
In xxxHOLiC Rou it's revealed that Doumeki forsook science to study minzokugaku, a choice that Tsurugi Kohane made as well; the discipline that Yanagita founded reached its height in the 1930s, and their decision only throws the fact that in xxxHOLiC CLAMP never use the word "youkai" into sharper relief. Terms such as 'mono' and 'ayakashii' and 'yuurei' appear frequently, but their all-purpose signifier has been expunged. Doumeki and Kohane might reasonably have chosen to major in youkaigaku but for the fact that such a choice would undoubtedly bring home to the readers xxxHOLiC's status as a youkai manga in a way that might very well destabilize the suspension of disbelief or ironic imagination necessary for readers to enjoy the work.
Nevertheless, it is clear that HOLiC is a youkai manga, insistently locating a nexus of the mysterious and the weird (Watanuki's shop) in the middle of present-day Tokyo and finding mysterious things both in customs kept alive only in the otherworld and in insistently contemporary devices such as computers and the TV.
The other thought I had, in light of Foster's discussion of the kuchi-sake-onna, a new youkai who terrorized Japan in the late 70s and early 80s, is whether or not Li'l Slugger of Kon Satoshi's anime Paranoia Agent might be considered a youkai. Given the fact that he is both a harbinger, an instantiation of and a resistor against the contemporary social problems detailed in the anime, and that he generally appears only at twilight or at night and only when his victims are alone, Li'l Slugger's status as a deliberately created, mediated youkai seems clear.
Foster, Michael Dylan. Pandemonium and Parade: Japanese Monsters and the Culture of Youkai. Berkeley: University of California Press, 2009.
--------------. "The Otherworlds of Mizuki Shigeru." Mechademia 3 (2008): 8-28.