There has been a lot of buzz in the (scientific) twitter/blogo-sphere regarding this. The main point of contention is essentialy the % of functional element ENCODE annotates. As it turns out, their criteria of denoting a DNA element as 'functional' is debatable (i.e. a DNA sequence with biochemical activity). These elements when deleted from the genome often has no visible phenotypic change to the organism (us), which is why the % they put is believed to be way too much.
Maybe not observable effects. There so many tiny things that must be in our genes that switches that affect anatomy are probably a small percentage. For example, the way people's laughs sound or the fact that almost everyone is attracted to paradisiacal places are probably influenced by genes and not just culture and nurture.
That is one possibility. But with subtle things like that, the trick is to come up with an experiment that either supports or falsifies them. Until such data exist, it remains a mere hypothesis.
Here's a recent excellent blog post on the issue, in readable form to the layman: http://selab.janelia.org/people/eddys/blog/?p=683