Worth noting is the pullout poster in the Genome issue of Science (this week). It details how the chromosomes have been sliced and diced across 21 different species, pointing out those that are closer in terms of recent evolutionary divergence have the greatest similarity in their chromosomes.
For example Human 11 ~= Chimp 9 ~= Cow 15 ~= Sheep 15 but as you get further away, things start turning into hash. The rat and mouse genomes are *really* reshuffled and the Zebrafish is totally different. But when all is said and done, we will have a moderately complete set of the insertions, deletions, transpositions, breaks, recombinations, etc. that have occured to produce the different species.
Now of course the creationists will simply say that it was "created" that way....
It will take us a while to get there, since we are now about to the point where private+public labs can do about 2 large genomes per year. But by 2010 or so we should have the major economic crops & animals done and will have maybe made a dent in those organisms that have really interesting properties of interest to us (longevity, oxygen tolerance, limb regrowth, etc.).