In the 1970s, before the advent of VHS tapes, the BBC deemed many programs no longer valuable. To make room for newer programs, they simply destroyed the old ones. Doctor Who was one of the series affected, with many early stories from the '60s now either incomplete or missing entirely.
Despite this, the stories still survived mainly through the Target Books series of novelizations, although quite a few of them are now out of print.
Missing stories survived in other ways, from audio recordings made by fans to telesnaps to shooting scripts.
If you'd like to explore these lost stories, here are some valuable links:
Photonovels
"Recreations of the classic 'missing' Doctor Who adventures, using images, sounds and video clips."
The Doctor Who Scripts Project
Transcripts of all missing stories from the First and Second Doctors, plus a few extras.