Well a study just came out that there are lots of little non-coding RNAs expressed in interesting patterns in the Brain. I've actaully heard about similar unpublished data from some other sources.
Does this mean that the genome is filled with functional ncRNA encoding genes? Hold your horses. As noted elsewhere, these little bits of RNA represent less than 1% of the genome. Moreover no function has been ascribed to them (perhaps they are negative or positive regulators of gene expression?) Third, many studies iindicate that 50-70% of the genome is transcribed as primary transcripts - so are these longer lived ncRNAs the products of overactive cryptic transcriptional start sites coupled with the particular array of transcription factors present in any given cell type? Are these just RNAs that survive the particular RNA processing proteins expressed in any given cell type? Are these the product of transcriptional noise + RNA processing noise?
Someone needs to perform a functional experiment.