Are you running a Wide Gamut monitor with a ICC ColorSync profile by chance?
If you are, the dock- for some reason utterly beyond me- "caches" the un-corrected version of the icon (so the ColorSync profile does not apply to it).
In this case, the app folder is what the other two folders SHOULD look like, because it was dragged into the dock after you enabled your monitor profile.
If you drag the Documents and Downloads icons off the dock, then re-add them from the Finder, they'll have the same colour as the App folder. I had the exact same issue in both 10.6 and 10.7.
-SC