I think people get emotive over the term 'junk'. It was always just a phrase rather than a technical description. We know that ~80%, maybe a little more, of the genome does not show conservation. If the function was important to the survival of the organism it have been selected for and thus evolutionarily conserved - hence the 85% "junk" figure. This does not mean that it isn't entirely biochemically inactive, or that there are some longer range periodicities in the sequence that are not elucidated. And as another commenter has noted, about half of the genome is composed of remnants of the Alu element, which jump about occasionally, but mostly degrade into total inactivity (sometimes being reactivated by recombining broken parts together).

What has gained a lot of attention was the massive ENCODE project, which sought to provide a detailed atlas of biochemical function in the human genome. The headline figure from there has been that 80% of the human genome has some function. There's a lot of controversy (understatement hat on) on the basic experimentation done for ENCODE, the structure of the project, the usefulness of the data produced and how they define biological activity.

The debate possibly got a bit out of control - the most sarcastic peer reviewed article I have ever read stirred the pot a bit (for more info: http://www.scilogs.com/next_regeneration/the-encode-controve...). I think most biologists (warning, personal opinion) would still hold that 80% of the genome is not meaningfully biologically functional.