Source code is text that describes a computer program in a (human-readable) programming language. It consists of one or more text files. In modern software development, machine code is used only in a very small number of areas; most development is done by compiling source code written in high-level languages. Software and its accompanying source code generally carry a license that falls broadly into one of two categories: free software or proprietary software.
LLVM is a remarkably clear code base. Very complex, but beautifully organized
Principia source code: a comprehensive unit system and effective use of Unicode
SerenityOS: code that delightfully structures things you would not expect to be possible in C++. Much of the code was recorded on YouTube as it was written, so you can watch and listen to the process that led to the final product
Through the metaprogramming used in Django's Model and Query objects, I could learn how Python works internally
Perter Norvig's spell checker
Factorio (game): amazing that a small team made such a solid, performant, and addictive game. Also runs an excellent developer blog
Emacs: it has some odd APIs, but Emacs's design is remarkably effective. The way you customize interactive modes for individual buffers is clever and beautiful.
Remember the Milk: cheap, fast, and effective; its intuitive, ergonomic UI design keeps impressing
Rollercoaster Tycoon: beautiful, performant assembly code written almost entirely by hand by one person
Syncthing: is there any other open source this good?
Turbo Vision/Turbo Pascal for MS-DOS: the best object-oriented library. Its successor, Delphi for Windows, was the most productive environment
SQLite: the best small software. People often call it "an alternative to fopen()"