1. General: "Roofing Solutions: Reference Manual for Property Managers, Owners, Architects, and Specifiers" is an excellent introductory guide to roof maintenance, and effectively explains the bottom line value of a roof maintenance program. It is made available by the GAF Materials Corporation.
2. General: "Life-Cycle Costs of Commercial Roof Systems", a paper available at the website of Carnegie Mellon University's Green Design Institute, provides useful information.
3. Built-up Roofs: "ROOFER: An Engineered Management System (EMS) for Bituminous Built-Up Roofs" is an extremely detailed and valuable resource put together by the US Army Corps of Engineers' Engineer Research and Development Center. Discussion of the pros and cons of repair vs. replacement starts around page 42 and goes on for some time.