I recently stumbled across a paper proposing a set of mammalian genomes for sequencing to further aging research. A free version of the proposal can be found via this site. I had previously posted some ponderings about what the most interesting unsequenced genomes are, and this would be one focused take on that question.
Despite the fact that it is clearly a process I will be familiar with, I'll confess a lot of ignorance about aging. The paper lays out a good rationale for the mammals it chooses (though with a mammalian focus, misses the opportunity to sequence the tortoise genome!).
This paper is also worth noting as something we will not see many more of. Not because there aren't plenty of interesting genomes to sequence, but because it won't be worth writing a paper about your plans to do so. Once genome sequencing becomes very cheap, a proposal to sequence a mammalian genome will become just a paragraph in a grant proposal at most, or more likely something mentioned only after the fact in an annual grant report. Certainly in the world of small genomes, such as bacteria, the trouble will be getting the samples to sequence, not the cost of sequencing.
On the other hand, even with really cheap genome sequencing, it will be a long time before all species are done -- even if some scientist has an inordinate fondness for beetle genomes!