Sigh - I was going to recommend this piece about recent human genome research in Scientific American, by a leading researcher in comparative genomics, Katherine Pollard, until I came to the last paragraph:

Experimental and computational studies now under way in thousands of labs around the world promise to elucidate what is going on in the 98.5 percent of our genome that does not code for proteins. It is looking less and less like junk every day.

Anyone, especially a genome scientist, who implies that most of our genome is packed full of functional sequences should back that up with some specifics, starting with answers to these two questions:
What makes you think that most of the 1 million alu elements in the genome are functional?

Ryan Gregory's onion test: Why does an onion need five times more non-coding DNA than a human? In fact, why does one species in the onion genus need almost five times as much non-coding DNA as a closely related species?

Just to reiterate: of course there are more functional non-coding sequences in the human genome waiting to be identified. But those who set out to find function in all or most of the genome are engaging in a giant, molecular snipe hunt.