The easiest way to upgrade to the latest version of ImageJ is to use the Help>Update ImageJ command, available in version 1.41 or later. Use the ImageJ Updater plugin to upgrade earlier versions.
The Update ImageJ command downloads the latest jar file (ij.jar) from imagej.nih.gov/ij/upgrade/ij.jar. It downloads the "daily build" jar file from wsr.imagej.net/download/daily-build. The Java source code is available at image.nih.gov/ij/download/src/.