A commenter named "Kilian Klaiber" in a comments thread on Jihad Watch back in July had an interesting hypothesis about a "peculiarity in Islam" -- which he describes with a couple of questions:
"Why is a stone venerated in the Kaaba and why is it placed into the corner of the building?"
And his hypothetical answer?
"Well, the corner stone originally stands for Jesus. Ephesians 2:20 -- And are built upon the foundation of the apostles and prophets, Jesus Christ himself being the chief corner stone; Also see Psalm 118:22 -- The stone the builders refused has become the head [stone] of the corner. The Kaaba," so he goes on, unfolding his conclusion, "was originally constructed as a church. It had an apsis and the direction of prayer in the Kaaba was Jerusalem."