First, find out what your main class is, the one whose public static void main(String args[]) method is called. It doesn't neccesarily have to have a package name. It could be something like "com.blah.Game" or simply "Test"
Make a manifest file, which is a plain text file typically called "Manifest.mf". Add a single line to that file that looks like either of:
Main-Class: com.blah.Game
or
Main-Class: Test
(as was explained above for finding your main class' name.
Then just do like hsvmoon explained, and do the following:
1. Open a terminal and cd to wherever the .class files are, or the root of where they go. If you don't use package names, then cd to where all the .class files are. If you do use packages, then go to the directory where the packages begin, so if your package name is "com.blah", go to the parent directory of the "com" directory
2. Type "jar cvfm path-to-Manifest.mf *"