Pico is an open source CMS application that is capable of very few things. It uses flat-files as the database and built with PHP. Simply, there is no setup and the app works instantly.
Medoo is a lightweight (~8kb) PHP framework for working with SQL databases. The framework comes as a single file and works withВ MySQL, MSSQL, PostgreSQL,В SQLite (and more).
In order to manage MongoDB databases easily, Genghis, a single-file, self-hosted and web-based solution is pretty handy. It can be installed either as a Ruby gem or as a standalone PHP script.
Koken is a free and self-hosted CMS (PHP-MySQL) that is focused on building websites where portfolio/gallery is in the core (like designer or photographer sites).
BugKick is an open source bug tracking and task management application (source is hosted on GitHub) that is “light” in means of features (which i sometimes nice).