First I'd better apologise for the confusion of having a BiBTex style sheet available when we don't accept TeX/PDF submissions. That style sheet is really for use on the other PLoS journals which can handle TeX submissions, sort of. It is on the PLoS ONE Guidelines for Authors by mistake and I haven't had a chance to edit it out yet.

As to handling LaTeX/pdf submissions that is something we have been trying to resolve for months. I'd really like to find a way to be more friendly to the LaTeX-using community, but at this moment I just can't.

The plain fact is that the production system we are using can only accept Word and RTF files (and possibly Open Office documents although we have never had the opportunity to test this). I desperately would like to be able to accept LaTeX files but there is just no way to reliably process them to produce XML conforming to the DTD that we (and PubMed Central) use. LaTeX converters do exist but none that we have tried (and we have tried all the ones we know about) are sufficiently reliable. The big problem is with the equation handling which is of course what LaTeX does best.

For PLoS ONE to function it is vital that manuscripts can be checked and signed off by authors before they enter the production process. The alternative is intensive manual subediting and proofing. That would make it impossible to scale the journal to high volumes, at least double the production time (although more likely the lack of an ability to scale would mean that backlogs would build up), and approximately double the cost to authors.

The only work around that we can offer is to point authors in the direction of the best LaTex converters that we know about. They are pretty good but the resulting files need to be checked carefully especially the equations. We have been trying to put together some instructions for how to convert LaTeX to RTF and the current draft is attached below.

LaTex Converters

TeX2Word
LaTeX2RTF
TexConverter
TexPort
CambridgeDocs

Before converting your paper to Word/RTF:

Combine all sections of the file into a single file; do not submit separate .bbl or .bib files. (See BiBTeX instructions below.) Avoid use of personalized macros and shortcuts (e.g., \newcommand, \def). The TeX file must contain expanded versions of shortcuts and macros.
Please comment out any graphics and table files (e.g., \includegraphics, \figbox); all images must be submitted as separate .eps or .tif files and all tables must be submitted as separate editable word or excel files.
If you use BiBTeX:

1. Run LaTeX on your LaTeX file.
2. Run BiBTeX on your LaTeX file.
3. Open the new .bbl file containing the reference list and copy all the contents into your LaTeX file after the acknowledgments section.
4. Comment out the old \bibliographystyle and \bibliography commands. Run LaTeX on your new file before submitting.

The best way to view equations will be to use MathType (not vital, just helpful). Anyone can download the free "trial" version at http://www.dessci.com/en/products/mathtype/trial.asp. Any equation editor can be used, however. As long as the equations open in Word, they should be okay.

Once the file has been converted, please check the following:

1. Please make sure that footnotes are incorporated into the text
2. Check to see that references are complete and in order. References may have dropped out in the conversion if they were added later in your writing/editing process and not inserted correctly. Often the reference tag from the TeX file will remain at the end of each line as an artifact. All extraneous text should be deleted. It might look something like this:

   [45] Orr HA (2005) The Genetic Theory of Adaptation: A Brief History. Nature Reviews Genetics 6:119–127. orrNRG2005Key: orrNRG2005 Annotation

3. Please check all numbered citations throughout the paper (including figures and tables).
4. Figure captions need to be listed at the end of the paper. Check that they are there.
5. Scan the paper for misspellings. The conversion often takes spaces out of the text so that two words are pushed together (ie, “about a” will become “abouta”). There shouldn’t be too many of these, and they should be relatively easy to find.
6. Please check all special characters to make sure that these are appearing as they should. If you need to change any of the characters, you can use the “insert symbol” found in the “Insert” menu.
7. Numbered equations (equations set apart from paragraph text) should automatically appear in math boxes. If they are not appearing, please retype them (using an equation editor such as MathType).

Sorry that this isn't the concise and positive answer that you were hoping for but it is the best we can do right now.