I second Gomo and Botanicula, those are perfect. I would add:
Little Inferno - funny, unique, charming, with some rather simple puzzles, but I think they should be engaging and funny enough to a 6 year old.
Any and all parts of the
braveland series - it's basically a very simple version of Heroes of Might and Magic or King's Bounty. The graphics should quite fitting for a kid, and as the difficulty is rather low for a turn based strategy game it should be about right.
LOOM - ok, here I'm kind of guessing, not having any experience with kids outside of having been one a while back :P. It might prove too complex for a little kid. Then again it's actually a fair bit easier than most classic adventure games, and I think it's the perfect kind of fantasy story for a child, one with a unique world and atmosphere and ideas, and even if won't "get" it all, it will still challenge and stimulate his imagination.