What should be the next genome sequenced? Olivia Judson has turned this question into an analog of Fantasy Baseball. Submit your suggestions to her/the world at The Fantasy Genome Project - Olivia Judson Blog - NYTimes.com
Or submit them here. For microbes it is so cheap that there is no point in doing this type of competition (e.g., for a bacterial isolate it would cost ~ 1-2000$$$ to do the shotgun sequencing for most species and then if you want to finish it would cost more, but still not very much)
My suggestion for a bigger genome to do that would be fun, interesting and important --- the blue whale. Biggest animal on the planet. Ever. Just must have its genome.