Turbo late, but...

LibreOffice sounds like it would have easily checked off most of your troubles. It has a command line switch to convert documents to PDF and some basic support for DOC(X)/XLS(X)/PPT(X)/&c. Some tool called `docx2txt` might also work for some basic documents. Overall I haven't had any professors complain about the fact I upload all my documents and slideshows in PDF and they have also been considerate and provided me a PDF of whatever they hand out upon request.

No offense but until you know exactly what you want, know your tools very well, a WSYIWY{G,M} tool will be your best bet if only for discoverability and instant preview. Still want to deal with (La)TeX? LyX has been incredibly useful in that regard.

But alas, documents aren't your main problem. The real enemy lies in those that oppose a free/open workflow and by that I specifically am referring to DRM-riddled tire fires and certain Web sites that will refuse to work on a *NIX system either by malice or lack of support. I'd advise a separate Windows machine (virtual or not) to work around that, as much as you might not be fond of the idea.