The BBC also incinerated film copies of the episodes. My understanding is that this was done in order to save space in their archive. (I remember something about a leaking roof.)
When foreign stations licensed the show, they were sent copies of the episodes with instructions to return them or destroy them after broadcast. A number of episodes that survived did so because those stations failed to follow through. They violated the BBC's copyright (presumably unintentionally due to poor license compliance). Ironically, such episodes survived because of copyright infringement.
Beyond the loss of Web material like the Hitchhiker's Guide site, or of software for no longe obtainable platforms, I fear we may face a similar situation in the future due to DRM. The Doctor Who case demonstrates that the copyright holder cannot always be trusted with preservation of significant works[1], and copying is the best insurance against destruction.
[1] I emphasize significant works, by which I particularly mean those that are distributed widely. (Not personal journal articles as mentioned by another poster.) When works are distributed to the public, the public gains an interest in them. This interest is not reflected in law, but it does exist. (Indeed, I would argue that this interest arises because the public, through its activities of interpretation and evangelism, creates much of the value of such works. Think Star Wars or Rocky Horror.)