A free encyclopedia, like any other form of free knowledge, can be freely read, without getting permission from anyone. Free knowledge can be freely shared with others. Free knowledge can be adapted to your own needs. And your adapted versions can be freely shared with others.
Wikipedia produces a massive website filled with an astounding variety of knowledge. If it were to produce this website using proprietary software, it would place potentially insurmountable obstacles in front of those who would like to take our knowledge and do the same thing that we are doing. If you need to get permission from a proprietary software vendor in order to create your own copy of our works, then you are not really free.
For the case of proprietary file formats, the situation is even worse. It could be argued that as long as Wikimedia content can be loaded into some existing free software easily enough, then its internal use of proprietary software is not so bad. Offering information in a proprietary or patent-encumbered format, violates the commitment to freedom and forces others who want to use "free knowledge" to use proprietary software themselves, which limits their freedom.
The Wikimedia community aims to be the vanguard of a knowledge revolution that will transform the world. They are the leading edge innovators and leaders of what is becoming a global movement to free knowledge from proprietary constraints. A hundred years from now, the idea of a proprietary textbook or encyclopedia will sound as quaint and remote as we now think of the use of leeches in medical science.
Through this work, every single person on the planet will have easy low cost access to free knowledge to empower them to do whatever it is that they want to do. Wikipedia (along with its sister projects) has become one of the largest websites in the world using a model of love and co-operation that is still almost completely unknown to the wider world. But it is becoming known, for both its principles and achievements – because it is the principles that make the achievements possible.
That is why the Wikimedia Foundation always uses free software on all computers that it owns, and that it always puts forward its best effort to ensure that free knowledge really is free, in that people are not forced to use proprietary software in order to read, modify, and redistribute it as they see fit.