I've been hearing rumors that the NHGRI is no longer accepting white papers for genome projects (I can't find anything on this at the NHGRI webpage). They will be shifting their focus toward other projects, including large scale polymorphism studies. Instead of white papers, grant proposals (submitted to NIH, I presume) will be required to fund whole genome sequencing projects.
I haven't heard anything from the NHGRI, but it's no secret that the priorities in all the major genome centers are shifting to resequencing projects. There will still be some sequencing of new organisms, but those pipelines are so fast and so well established that they're hardly even news any more. (How much press did the sea urchin genome get?)
Last I heard, a human genome is going for around $500k, and as 454 pyrosequencing and Solexa technologies take off, the cost is going down considerably. If they aren't already, sequencing new organisms will be well within an NIH grant in a year or two.
As you said, the big push now is to identify genomic variation, so that disease loci can be identified and eventually, the era of personalized medicine can be ushered in. The Cancer genome project is just launching, and there's talk of a Human Variome Project, which is a little more amorphous at the present.
I'm probably a bit biased by my research focus, but it seems sensible that the NHGRI research money is being funneled to the cutting edge stuff, rather than towards cranking out more new genomes that won't have much immediate application. From a biomedical perspective, it makes more sense to tackle projects that are likely to have clinical applications in the relatively near future. I have little doubt that sequencing companies and spare pipeline cycles will easily be able to produce the novel sequences that people ask for.
Edit: Those last few sentences are the parts that may get me berated by all the classical geneticists for being human-centric, but hey - I'm a realist. When there are limited grant dollars, research with immediate application to human health always rises to the top of the stack.