Below is a cool piece, reposted from the Wares Lab. I run into this issue too and I think the answer is modern journals like PeerJ that allow movies plugged right into the paper.
When I first started doing science, visualization of our data and results was a bit easier. Sequence a gene from 20-30 individuals, generate a phylogenetic hypothesis, make it look pretty, Figure 1. As we have moved to information from more and more loci (or greater numbers of samples, or any other factor of additional complexity), there have been ways developed to summarize the results visually for the purposes of proving to the audience of a journal article that you are on the right track in terms of interpretation. For example, former postdoc (and now faculty at Texas A&M – Galveston) Ron Eytan used these images to show which parts of a phylogeny were consistently supported and which were not (an image that overlays many reconstructions of a phylogeny from the same data):
and we are now becoming familiar with things like transcriptome heat maps to illustrate over/under expression of particular genes:
and to an extent, we have just become accustomed to more complicated representations of data and results residing only as online supplemental files. In other words, often the most important components of science are no longer able to be represented in the standard peer-reviewed journal article. We are at this point often having to take into consideration representation of science through multiple filters: how will it communicate to the audience? what if that audience is looking only at a photocopy, or black-and-white print of my article? what if that audience is unable to afford the journal I submit to?
Read the rest and see a video-result example here.