In its 20-year history, arXiv has gone from a small physics pre-print repository to a giant archive widely used in many disciplines, and so trusted that it sometimes almost acts as a de facto journal [*]. Its growing body of literature on statistical phylogenetics is sure to boom anytime now.
The way I see it, placement of pre-prints on arXiv is a terrific idea. It (a) provides a good way to 'air out' a manuscript, and obtain feedback in case something is wrong, (b) you can cite your permanent arXiv article ID from the time of submission, (c) a version of the manuscript, unadulterated by (what may have been in your opinion) the unfair mauling it got in review, while still being able to correct errors. All the while, it does not interfere with peer-reviewed journal publication, and your manuscript is out instantly.
Most publishers' policies allow the archiving of pre-review manuscripts (including Nature, Science, PLoS, PNAS, PRSoc, Evolution, SystBiol, AmNat, etc.). Some allow post-review manuscripts to posted, as well. Individual journal policies can be checked at SHERPA/ROMEO, which also contains policies for personal/lab website posting and compliance data for funding agency requirements. My next paper is going here.
Try searching arXiv directly, go to their Populations and Evolution collection within Quantitative Biology, or click around to see and arbitrarily chosen sample author. The submission process is reasonable, and one can even submit PDFs generated from MSWord docs (as well as TeX files, and a couple of other formats).
* Perhaps most famously, it is the only place that hosts Grigori Perelman's three-part proof of the Poincaré conjecture [1,2,3; references listed for those who, unlike me, may be both interested and able to understand algebraic topology], which sits on arXiv without a formal peer-review process. He was eventually awarded the Fields Medal that he famously refused.