“Ignorance, the root and stem of all evil.”

Source: Rich Dad, Poor Dad: What the Rich Teach Their Children About Money That the Poor and Middle Class Don't

This appears in Twain's posthumous The Refuge of the Derelicts (1905), but it had already been published by other writers.
The earliest citation found in Google Books is a 1872 article by Richard Bowker: "Our Crime Against Crimes" https://books.google.com/books?id=YZgBAAAAYAAJ&pg=PA68&dq=The+lack+of+money+is+the+root+of+all+evil&hl=en&sa=X&ved=0ahUKEwjWi5DE1crLAhUI3mMKHeSdB0YQ6AEIKzAB#v=onepage&q=%22lack%20of%20money%22&f=false, in The Herald of Health, vol. 19 no. 2, New York: Wood & Holbrook, February 1872. The saying is placed within quotation marks, perhaps indicating that it was already well-known.
A precursor is found in an article from 1859 https://books.google.com/books?id=gpdEAQAAMAAJ&pg=PA209&dq=The+lack+of+money+is+the+root+of+all+evil&hl=en&sa=X&ved=0ahUKEwjWi5DE1crLAhUI3mMKHeSdB0YQ6AEINTAD#v=onepage&q=%22lack%20of%20gold%22&f=false: It is very well to repeat, parrot-like, the old axiom that “the love of gold is the root of all evil;” but it is very certain that in truth—the lack of gold is the great incentive to crime.
Disputed

Quote due to Donald Knuth, "Structured Programming with Goto Statements" http://pplab.snu.ac.kr/courses/adv_pl05/papers/p261-knuth.pdf, Computing Surveys 6:4 (December 1974), pp. 261–301, §1. Knuth refers to it as "Hoare's Dictum" 15 years later in "The Errors of TeX", Software—Practice & Experience 19:7 (July 1989), pp. 607–685. However, the attribution to Hoare is doubtful. http://shreevatsa.wordpress.com/2008/05/16/premature-optimization-is-the-root-of-all-evil/
Attributed

"Irrationality is the Square Root of All Evil" (Sep, 1983) Scientific American 249 (3) article reprinted in Metamagical Themas (1985)

Source: Short fiction, The Early Asimov Book One (1972), Half-Breed (p. 160)

Source: Either/Or: A Fragment of Life