Arthur Allen at Slate goes with both barrels after the Human Genome Project, basically asking where are the instant cures which were promised during the effort. His tag line at the end reads, "for this you should pay $500?"
Allen has no idea. $500 per taxpayer is a TINY amount of money (and I should point out that the Celera efforts were even cheaper, and done on the stockholder's dime). But yes, if he'd rather have half a flat-screen TV so he can watch Lost, well, I guess that's his prerogative.
I would agree with Allen that the disease side of the human genome project was badly oversold, but the feeling on the basic science side is that the genome efforts (plural; Allen is ignoring the C. Elegans and Drosophila efforts which built up to the human sequence) remain an epochal event. The methodology of shotgun sequencing alone has had applications in microbial, environmental and ancient DNA sequencing, which in turn has greatly increased understanding of things like the extent of horizontal gene transfer among species and the contribution of phage to open-ocean ecosystems. The combination of exponentially growing databases and cheap, cheap sequencing is allowing whole new sets of questions to be looked at rigorously. And newer sequencing methods are coming in which will blow the current methods away.
The genome efforts also played midwife to a cultural change in the basic biology mindset. I remember a lecture Gerry Rubin gave, in 1998 or so, talking about knowing "all the genes in Drosophila" and thinking he was crazy. Now people talk all the time about the transcriptome, the proteome, etc, with the intent of knowing all the elements present in an organism at a single timepoint. It's doable now, and is seen as doable. I remain a one-gene-one-scientist person, but I would be crazy not to be following this work.
With respect to human biology, the availabilty of the genome has indeed allowed identification of nucleotide stretches associated with human variation-- disease, for Mr. Allen. The Tourette's syndrome paper from last week, and earlier studies of longevity associated genes were only found because the human genome scaffold is precise enough to detect small scale inversions.
I think that's $500 well spent indeed.