John Mattick, University of Queensland, is one of the leading proponents of the idea that much -- perhaps most -- of the human genome is functional. He has been making claims along these lines for at least 15 years, but seems to always present it as a new idea. Readers of this blog may also remember the Dog's Ass Plot included in one of his publications. 

Anyway, he has done an interview with BioMed Central about his thoughts on non-coding DNA, regulatory RNA, etc.

A transcript is available here in PDF. Note this statement in particular:

You mentioned earlier the possible significance of transposons. What part do you think they have played?

That is one of my many favourite topics. It is widely assumed - though not by everybody - that transposon-derived sequences are simply 'selfish' mobile genetic elements that have no function other than their own propagation. Books have been written about such things, and that is indeed one possibility. But the raw material for evolution is duplication and transposition, with the latter having the great advantage of being able to distribute functional cassettes. So it's equally possible that a large fraction of the transposon-derived sequences that are in our genome are actually functional.
I have said it before, and I will say it again. The possibility that many transposable elements would be co-opted for organism-level functions has been around since the beginning of the "selfish DNA" idea. Moreover, the point of introducing the concept of selfish DNA in the first place was prompted by the standard assumption that just being present implied a function for all DNA.
"It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another." (Orgel and Crick 1980)

"In our recent experience most people will agree, after discussion, that ignorant DNA, parasitic DNA, symbiotic DNA (that is, parasitic DNA which has become useful to the organism) and ‘dead’ DNA of one sort or another are all likely to be present in the chromosomes of higher organisms. Where people differ is in their estimates of the relative amounts. We feel that this can only be decided by experiment." (Orgel et al. 1980)
One can find examples like this all the way back to the earliest discussions of non-coding DNA. It simply is NOT TRUE that non-coding DNA was dismissed as functionless.