MilkyTracker - MilkyTracker is an open source, multi-platform music application for creating .MOD and .
OpenMPT - OpenMPT is a popular tracker software for Windows.
SunVox - SunVox is a small, fast and powerful modular synthesizer with pattern based sequencer (tracker).
musagi - Musagi is a complex music authoring and synthesizer similar to trackers.
PxTone Collage - A music editing software, capable of using common sounds, custom sounds, and everything in between to make surprisingly good music. Originally in Japanese, but easily fixed.
BassoonTracker - Web-based Amiga music tracker in JavaScript