For your documentation, you can any any format that can be fully used with free software.
LaTeX is OK. Texinfo is OK. ODT (Open Document Text, used by OpenOffice.org 2) is OK. Flash is not until there are good enough free software tools to generate and read them.
Word and RTF are not accepted - they can be used with OpenOffice.org but the best way to edit those files (without any incompatibility) is still to use proprietary software, so using those formats entices people to use such software. Use directly ODT intead.
HTML is OK as long as it comes with the source format (eg. if you used DocBook to generate HTML pages, you need to publish the DocBook as well, not only the HTML). If HTML is the source format, then no problem, as long as it doesn't require the feature of a proprietary browser to work.