Although leadership is essential for shepherding the oranizational and discipleship structures of the church, the strucutres/systems/cultures—and not leadership—are the focus of this list. Each of these books offers something unique, but any one of them will help a great deal if read and applied well.
The Book of Church Order of the Orthodox Presbyterian Church
Hearers and Doers: A Pastor’s Guide to Making Disciples Through Scripture and Doctrine by Kevin J. Vanhoozer
The Trellis and the Vine: The Ministry Mind-shift That Changes Everything by Colin Marshall and Tony Payne
The Whole Systems Approach: Involving Everyone in the Company to Transform and Run Your Business by W. A. Adams, Cindy Adams with Michael Bowker
An Everyone Culture: Becoming a Deliberately Developmental Organization by Robert Kegan and Lisa Laskow Lahey
The Gospel Commission: Recovering God’s Strategy for Making Disciples by Michael Horton
Evangelism: How the Whole Church Speaks of Jesus by J. Mack Stiles
If you are looking for help with a specific topic, there are so many good resources. But here are a couple good places to start:
Faithful and Fruitful: Essays for Elders and Deacons ed. by William Boekestein and Steven Swets
Various articles in Ordained Servant. Check the subject index.