One of the big motivating factors in setting up Methods in Ecology and Evolution was the recognition that there are lots of ways to present research (without losing sight of the importance of peer review, rigour, and quality assurance).
However in terms of uptake and usage, the problem with the conventional paper is that it is not necessarily tailored to conveying research in a quick and convenient manner. For ‘methods’ papers a big problem is that users need to understand how new approaches and tools work in practice and even to see examples of the method in action. The printed paper or pdf is not always the best way to do this.
Some publications are trying out different ways of presenting research. For example the Journal of Visualized Experiments is placing the emphasis on video presentation of research. There are some examples from Evolution and Ecology. For example, here is some research on visual sensitivity in lizards:
And here is something on applied ecology:
(you need to register to see the whole thing, but the clip should give a good introduction).
More generally I think that in writing methods papers we could do a lot more to ‘sell’ our methods. For instance, more ‘tutorial’-style supplements to papers, there being a mechanism for authors and readers to talk to each other, and for users to share their experience. By viewing these elements as a key part of the publication process everyone will benefit: authors will attract more readers, and users will find it easier to use new techniques.
Finally, and a bit more tongue in cheek this video includes an amusing take on the conventional publication process and the way that scientists conduct their debates via the literature (plus more!):