Zelda: The Sheikah are 'watching her back.'
Fortune-Teller: either a Sheikah, a Sheikah wanna-be, or a reference to the Sheikah as PureLocke stated
Howling Stone: [theory]After MM, Link went back to Hyrule and joined up with the Sheikah to defend the royal family from an invading force from the north and to prepare for assisting a new hero in case Ganondorf returns. (also notice that the hero's shade has only one eye. This could have been from the war and used as symbolism by the developers of his connection with the Sheikah.)[/theory]
Veran/Agahnim: I don't remember.
Another important eye to consider is the Twilight Realm eye:
My belief is that this is a modern form of the Sheikah eye, which is also represented in its older form on the throne and on the back of the fused shadow (which also has only one eye in the front where you'd expect two):
Obviously not every Sheikah was an interloper, but I think this is evidence of intent that all or most of the interlopers were Sheikah.