Functionality of extra DNA
It is now known that as much as 98% of the DNA in a genome is not directly involved in the production of proteins (see cartoon below). This non-coding DNA was originally termed "junk DNA," as it was thought to serve no purpose.
However, current thinking is that some at lest of the non-genic DNA does have a function, including structural stability (helping stabilize the DNA molecule) and affecting the level of gene expression (Andolfatto, 2005). Much ongoing research is now focusing on "junk" DNA.
For a good review, see: http://www.eurekalert.org/pub_releases/2005-07/cshl-lcg071205.php
See also: Andolfatto, 2005