I played around with a bunch of free software but they all lacked professional settings to fine tune the output.
I've found that the encoding can be done using QuickTime Pro on a Mac machine using this WebM and this OGG QuickTime components.
The WebM is a regular Mac installer. The OGG component need to be copied to your local (machine and/or user) Library/Component folder.
Now I have an OGG and a WebM setting dialog when I hit Command E in QuickTime and in any QuickTime supported application.
Additionally, There's a great free and open source software for Mac called Media Converter which allows a very quick and simple export to WebM, OGG, DNxHD, ProRes and pretty much whatever FFMPEG supports. The software is also extensible with many presets.