Aside from vital regulatory functions, the presence of long stretches of seemingly useless DNA at least can have one potential protective function: to protect the precious islands of protein-encoding genes.

Changes in these long non-coding DNA sequence will absorb the brunt of physical and chemical mutagens.

Just this week's Nature (London) reports a cover story about the decoding of genomic code (signposts in DNA sequences) for chromatin packaging (similar to file zipping).

I am sure more mysteries will be unraveled in the future about the "junk DNA".