Darning is a tool for managing a series or sequence of patches to a software source tree, in the same vein as quilt but with extended functionality. It supports advanced patch concepts such as file mode changes and copying/renaming files. The GUI is the primary interface and the most complete, but a command line interface is also provided with fewer features at this stage.
SafePatch lets you edit program files and track those changes creating "patches" which can later be reverted or reused in a different setup. It's written in PHP, but can patch non-PHP applications because no integration into their source code is required. A bundled Control Panel allows easy tracking, installing, reverting, and diffing of available patches. SafePatch has an intuitive text patch file syntax which is uniform for text and binary files and independent of the engine being patched, has default support for VQMod .xml patches and FluxBB README mods, is written in OOP and uses events (and thus is easily extensible), and doesn't need a database.