I think that he knew that Light had become Kira again in the end. But he also knew that there was a part of Light that wasn't Kira, if that makes sense. I thought the foot rub was sweet, and not at all sexual. Why do people have to take every single thing as sexual now-a-days? Isn't there friends who you love more than anything else and if they died you would never be the same? Light was L's first friend... that's got to mean something. I mean, they're practically the same, yet opposites at the same time. I agree with someone's theory somewhere below about L. His parents were probably dead, I'm pretty sure that's what the beginning church scene meant where a small kid was crying. I wish they would've given us more background about him; he was an interesting character.

Oh, L-chan! I literally wept for you this episode. And all you against the anti-foot-rub-scene; it was sweet. His last gesture of friendship before the end. (Sorry for the emotions, I adored L)