Charles Darwin was an Anglican, but by most accounts he appears to have been largely nominal in his affiliation with the Church of England. Darwin may be better classified as a Unitarian. He was a member of a Unitarian congregation which he attended regularly during at least part of his life.
During Darwin's lifetime, the Unitarian Church was considered a relatively mainstream Protestant Christian denomination, although many of its beliefs even then separated it from other Protestant denominations. Today Unitarianism (known since a merger as Unitarian-Universalism in many parts of the world) is considered a distinct religion and not a subset of Christianity, but during the time that Darwin lived, there was no concept of Unitarianism as a "non-Christian religion."
Darwin has been classified variously as deist and an agnostic. Of course, these are not religious affiliations in his case, but are classifications of his theological beliefs. Darwin was never a member of any Deist or Agnostic organizations.
From: "Religious Affiliations of Celebrities" page in "Celebrity Religion" section of "Religion Facts" website (http://www.religionfacts.com/celebrities/religions_of_celebrities.htm; viewed 20 April 2007):
Below is an index of the religious affiliations or belief systems of celebrities (both living and dead; in film, television, music, literature, academics and politics), listed in alphabetical order by last name...
Celebrity: Charles Darwin
Religion/Belief: Anglicanism/ Unitarianism
Quotes, More Information, Sources:
The evolutionary biologist was nominally an Anglican, but attended a Unitarian church. - Adherents.com [link to: http://www.adherents.com/people/pd/Charles_Darwin.html]