There is some overlap with the introductory resources found here. A list of advanced resources will appear shortly. Like the introductory resources these intermediate ones are all written from a broadly neo-Calvinist perspective and are books rather than articles.
The list is testimony to the comprehensiveness of neo-Calvinism.
Feel free to make suggestions in the comments.
James Nikel 2000. Mathematics: Is God Silent? Vallecito, CA: Ross House Books
Andrew M. Hartely 2008. Christian and Humanist Foundations for Statistical Inference. Resource Publications, Wipf and Stock.
M D Stafleu 2006. Relations and Characters in Protestant Philosophy. [online]
M D Stafleu 1980. Time and Again: A Systematic Analysis of the Foundations of Physics Toronto: Wedge Publishing Foundation.
M D Stafleu 1987. Theories at Work. Toronto: UPA.
Lydia Jaeger 2012. What the Heavens Declare. Eugene, OR: Cascade.
Nancy R. Pearcey and Charles B. Thaxton The Soul of Science Wheaton: Crossway Books
Jacob Klapwijk. 2008. Purpose in the Living World? : Creation and Emergent Evolution, Cambridge: Cambridge University Press.
Russell Maatman. 1993. The Impact of Evolutionary Theory: A Christian View. Dordt: Dordt College Press.
Geography and place
Henk Aay and Sander Griffioen (ed.)1998. Geography and Worldview: A Christian Reconnaissance. Toronto: UPA
Craig Bartholomew 2011. Where Mortals Dwell. Grand Rapids: Baker.
Environment and Green issues
Steven Bouma-Preiger 2001. For the Beauty of the Earth. Grand Rapids: Baker
Loren Wilkinson et al. 1980. Earthkeeping in the 90s. Grand Rapids: Eerdmans.
Eric O Jacobsen 2012. The Space Between: A Christian Engagement with the Built Environment. Grand Rapids: Baker.
Stephen V. Monsma, (ed). 1986. Responsible Technology: A Christian Perspective. Grand Rapids: Eerdmans.
Egbert Schuurman 1995. Perspectives on Technology and Culture Sioux Center: Dordt College Press.
Egbert Schuurman 1980.Technology and the Future - A Philosophical Challenge. Toronto: Wedge
Andrew Basden 2008. Philosophical Frameworks for Understanding Information Systems. IGI Publishing.
M C Smit 2002. Toward a Christian Conception of History. Edited and translated by Herbert Donald Morton and Harry Van Dyke. Toronto: UPA.
Mary Stewart Van Leeuwen 1985. The Person in Psychology: A Contemporary Christian Appraisal. Grand Rapids: Eerdmans.
Willem Ouweneel. 2008. Heart and Soul a Christian View of Psychology. Grand Rapids: Paidea Press.
Arnold H. De Graaff 1977. Views of Man and Psychology in Christian Perspective: some readings. Toronto: Institute for Christian Studies.
Language and Lingustics
Albert Weideman. Beyond Expression. Grand Rapids: Paideia Press.
David Smith with Barbara Cavill 2000. The Gift of the Stranger: Faith, Hospitality and Foreign Language Learning Grand Rapids: Eerdmans.
Alan Storkey 1979. A Christian Social Perspective. Leicester: IVP.
Herman Dooyeweerd A Christian Theory of Social Institutions. La Jolla: The Herman Dooyeweerd Foundation.
Bob Goudzwaard. Capitalism and Progress: A Diagnosis of Western Society. Grand Rapids: Eerdmans.
Alan Storkey Transforming Economics. London: SPCK/ Third Way Books.
David Koyzis 2003. Political Visions and Illusions. Downers Grove: IVP.
Jan Dengerink 1978. The Idea of Justice in Christian Perspective. Toronto: Wedge.
James Skillen 2013. The Good of Politics: A Biblical, Historical, and Contemporary Introduction. Grand Rapids: Baker, forthcoming.
Jeff Van Duzer 2010. Why Business Matters to God (And What Still Needs to Be Fixed) . Downers Grove: IVP Academic.
Art and aesthetics
Hilary Brand and Adrienne Dengerink 2001. Art and Soul: Signposts for Christians in the Arts Carlisle: Piquant.
Geoff Hall 2011. The Wilderness and the Desert of the Real. Upptacka Press (and others in the quadrilogy)
Calvin Seerveld 2000. Bearing Fresh Olive Leaves: Alternative Steps in Understanding Art. Carlisle: Piquant.
Karen A. De Mol. 1999. Sound Stewardship: How Shall Christians Think About Music? Sioux Center: Dordt College Press.
Hans Rookmaaker 2002. New Orleans Jazz, Mahalia Jackson and the Philosophy of Art: The Complete Works Vol 2. Carlisle: Piquant.
Quentin Schultze et al. 1991. Dancing in the Dark: Youth, Popular Culture and the Electronic Media. Eerdmans.
Doug Blomberg 2007. Wisdom and Curriculum: Christian Schooling After Postmodernity. Sioux Center: Dordt College Press.
John Van Dyk 2000. The Craft of Christian Teaching. Sioux Center: Dordt College Press.
Harro Van Brummelen 1992. Walking with God in the Classroom. Burlington, Ont: Welch.
Jack Mechielsen (ed.) 1980. No Icing on the Cake: Christian Foundations for Education. Brookes-Hall.
Stuart Fowler, et al. 1990. Christian Schooling: Education for Freedom. Potchefstroom: Potchefstroom University for Christian Higher Education.
Albert E. Greene Jr. 2003. Reclaiming the Future of Christian Education, Purposeful Design Publications; 2nd edition.
Michael P. Schutt 2007. Redeeming Law: Christian Calling and the Legal Profession. Downers Grove: InterVarsity Press.
Andre Troost The Christian Ethos. Bloemfontein: Patmos.
Theology and biblical studies
Gordon Spykman Refomational Theology. Grand Rapids: Eerdmans.
Michael Goheen 2011. A Light to the Nations. Grand Rapids: Baker.
Dave Beldman and Craig Bartholomew 2012. Hearing the Old Testament. Grand Rapids: Eerdmans.
Al Wolters 2005. Creation Regained. Grand Rapids: Eerdmans (2nd edn).
Richard Middleton and Brian J. Walsh Transforming Vision. Downers Grove: Inter-Varsity Press.
David K. Naugle 2002. Worldview. Grand Rapids: Eerdmans
Mike Goheen and Craig Bartholomew 2008. Living at the Crossroads. SPCK.
J. Mark Bertrand 2007. (Re)Thinking Worldview. Wheaton: Crossway.
John Peck and Charles Strohmer 2001. Uncommon Sense. London: SPCK.
John Byl and Tom Visker 1999. Physical Education, Sport and Wellness. Sioux Center: Dordt College Press.
Roy A. Clouser 2005. Myth of Neutrality. Notre Dame: UNDP (2nd edn).
Roy Clouser 1999. Knowing With the Heart. Downers Grove: IVP.
Andre Troost 2013. What is Reformational Philosophy? Grand Rapids: Paideia Press, 2013.
Steve Bishop (ed.) 2011. Like the First Gleam of Dawn: Reformational Studies - a B. J. van der Walt Reader. Potchefstroom: Institute for Contemporary Christianity in Africa.
Kornelius A. Bril 2005. Vollenhoven’s Problem-Historical Method. Sioux Center: Dordt College Press.
Herman Dooyeweerd In the Twilight of Western Thought. Grand Rapids: P&R
P Heintzman, G A van Andel and Tom Visker 1994. Christianity and Leisure: Issues in a Pluralistic Society. Sioux Center: Dordt College Press.
Media and film
William Romanowski 2007. Eyes Wide Open. Grand Rapids: Brazos.
Quentin J Schulte and Robert Woods (eds) 2008. Understanding Evangelical Media. Downers Grove: IVP.
Brian Godawa 2002. Hollywood Worldviews. Downers Grove: IVP.
Family and Marriage
James H. Olthius 1975. I Pledge You My Troth. San Francisco: Harper & Row.
James H. Olthius 1986. Keeping Our Troth. San Francisco: Harper & Row.
Alan Storkey 1996. Marriage and its Modern crisis: Repairing a Married Life. London: Hodder & Stoughton.
Harry Van Belle 1991. Two Shall Become One. Burlington, On: Welch Publishing.
Work and vocation
Amy L. Sherman 2011. Kingdom Calling. Downers Grove: IVP.
Lee Hardy 1990. The Fabric of This World. Grand Rapids: Eerdmans.
Elaine Storkey 2000. Created or Constructed? Milton Keynes: Paternoster Press
Mary Stewart van Leeuwen 1990. Gender and Grace. Downers Grove: Inter-Varsity Press.
Many of these books if they are in print are available from Byron Borger's Hearts & Minds Bookstore in the USA
Fuller bibliographies for most of the above areas are available here and here.