Version 4 is the latest and greatest version that maintains backwards compatibility with version 3 files. It started from version 3.x codebase that was upgraded to Java 8 in early 2020. It has better support for installation - in addition to the windows installer, universal ZIP package and universal installer, DIYLC now has a native application package for OSX available for download and is also regularly published to Flathub as a Flatpak distribution.
Version 3 is a relatively modern version that was re-written from scratch starting early 2010, but this time as an open source Java 5 project. It incorporates all the ideas that were accumulated over years and also better code architecture. That should provide better user experience, less bugs and code that's easier to maintain and extend.

Version 2 was re-written from scratch in Java mid 2007 and is platform independent. The big idea behind this version was flexibility - components were defined through XML files that explain what a component is and how it's rendered on the screen. Unfortunately, it was not very fast and was not backward compatible with version 1 which means that it cannot open files created with version 1. It was my first ever Java project, so code quality was not so great, which is why I gave it up at some point.

Version 1 started its life in May 2005 and was written in Delphi. As such, it only works on Windows machines (or through emulators). There's a large collection of layouts submitted by users for this version which is why it's still kept around. It was created primarily for guitar pedal circuits and has a limited set of components and functionalities.