Books describing the design and implementation of significant programs, all the way from overall philosophy down through the source code.
Side note: TheArchitectureOfConcurrentProgram? includes a quotation of ChristopherAlexander, which surprised me since the book was published in 1977! It also appears on RalphJohnson's GreatSoftwareBooks list.
Why does the reference to Alexander surprise you? There are mentions of his work on design in the proceedings of the original "software engineering" conferences, back in the late 60's
It surprised me because I didn't know that. :-)
The Practical Guide to Enterprise Architecture by JamesMcGovern also has good case studies on applying measures of goodness to large projects.
Don't forget LiterateProgramming books! The LCC book (A Retargetable C Compiler: Design and Implementation by Fraser and Hanson) is one great example. So is C Interfaces and Implementations - it's about how to write reusable libraries (with a focus on C), API design, etc. Highly recommended, whatever language(s) you use. --ScottVokes
PayrollExample discusses an arguable example of such.