For the purposes of this list, a "regeneration story" is one in which a regeneration is actually and initially depicted. For this reason The War Games is not included below, even though it is commonly thought of as a "regeneration story". It doesn't actually include a clear scene of regeneration, and the preponderance of stories in other media confirms that the Second Doctor did not regenerate at the end of it.
Additionally, immediate post-regeneration stories, like the 2005 Children in Need Special Born Again — and ones like Castrovalva, where the regeneration sequence was replayed — are not included.