PLoS Biology does point-counterpoint on whether our entire genomes are transcribed (and, by implication, whether the majority of our DNA is functional):
The Reality of Pervasive Transcription – Clark, et al.
Response – van Bakel, et al.
Interestingly, these two viewpoints tend to split somewhat cleanly between those who came into biology as computational people, and those who came in as experimentalists. (The split’s not perfect but the trend is there, and you can see it in the authorship of the two papers above.) Computational people (or, at least those who came in as computational people – I’m not making judgments about anyone’s experimental skills) are more likely to believe in pervasive transcription, and while others are more likely see it as experimental and biological noise.
Following the trend, I fall into the latter camp.