Primary sources
Søren Giversen, Apocryphon Johannis: The Coptic Text of the Apocryphon Johannis in the Nag Hammadi Codex II with Translation, Introduction and Commentary (Copenhagen, 1963)
The Facsimile Edition of the Nag Hammadi Codices: Codex II (E.J.Brill, 1974)
Bentley Layton, Volume Editor, Nag Hammadi Codex II, 2-7 (E.J.Brill, 1989) (2 vols)
Michael Waldstein & Frederik Wisse, eds, The Apocryphon of John: Synopsis of Nag Hammadi Codices II,1; III,1; and IV,1 with BG 8502,2 (E.J.Brill, 1995)
The Coptic Language
W.E. Crum, Coptic Dictionary (Oxford University Press, 1939, reprinted 2000)
[Caveat: Currently THE authority, it's also pricey, pre-Nag Hammadi, and pretty user-unfriendly.]
Thomas O. Lambdin, Introduction to Sahidic Coptic (Mercer University Press, 1983) ==>Amazon
Richard H. Smith, A Concise Coptic-English Lexicon, Second Edition (SBL, 2002) ==> SBL
History/Commentary, General
Elaine Pagels, The Gnostic Gospels (Random House, 1979)
[Caveat: Contains the erroneous early claim that there were 13 books in the jar.]
John Dart, The Jesus of Heresy and History: The Discovery and Meaning of the Nag Hammadi Gnostic Library (Harper & Row, 1988)
History/Commentary, The Gospel of Thomas
Stevan L. Davies, The Gospel of Thomas and Christian Wisdom (Seabury Press, 1983)
Marvin Meyer, The Gospel of Thomas: The Hidden Sayings of Jesus (HarperCollins, 1992)
Stephen J. Patterson, The Gospel of Thomas and Jesus (Polebridge Press, 1993)
Richard Valantasis, The Gospel of Thomas (Routledge, 1997)
Patterson, Robinson, and Bethge, The Fifth Gospel
(Trinity Press, 1998)
(The best all-around introduction. If you buy just one book, this is the one.)
Risto Uro, editor, Thomas at the Crossroads: Essays on the Gospel of Thomas (T&T Clark, 1998)
Stevan Davies, The Gospel of Thomas Annotated & Explained (Skylight Paths, 2002)
April DeConick, Recovering the Original Gospel of Thomas (T&T Clark, 2005)
April DeConick, The Original Gospel of Thomas in Translation (T&T Clark, 2007)
Other
Bentley Layton, The Gnostic Scriptures (Doubleday, 1987)
James M. Robinson, General Editor, The Nag Hammadi Library,
Revised Edition
(Harper & Row, 1988)(3rd ed.)(reprinted 1990 HarperCollins)
C. Wilfred Griggs, Early Egyptian Christianity: From Its Origins to 451 C.E. (E.J.Brill, 1990)
Kloppenborg, Meyer, Patterson, Steinhauser, Q-Thomas Reader (Polebridge Press, 1990)
Helmut Koester, Ancient Christian Gospels: Their History and Development (Trinity Press International, 1990)
Gregory J. Riley, Resurrection Reconsidered: Thomas and John in Controversy (Augsburg Fortress, 1995)
Robert W. Funk (The Jesus Seminar), The Five Gospels (Polebridge Press, 1993; HarperCollins paperback 1997)