EDuke32
EDuke32 is the one true decent Win32/*nix version of Duke aimed at modders, based on EDuke. It combines the work JonoF and Ken Silverman have put in to JFDuke3D with the work done by Matt Saettler on the original EDuke while adding tons of new, useful features.
EDuke32 is 99% compatible with all Duke3D 1.3D/1.5 and EDuke 2.0 mods. While most 1.3D/1.5/2.0 content will run fine, this functionality cannot be completely guaranteed -- for example, the default behavior for pipebombs changed between EDuke and EDuke32. As such, these features are offered only for the purpose of making it easier for modders to move their mods over to EDuke32. However, if you have a problem running an old mod, feel free to report it.