1. download jnemesis-1.1-jar.tar.gz
2. extract the archive (using WinZIP, or Ace etc)
3. Modify the file jnemesis.config so its looks like the one below:

NEMESIS=/C:/Program Files/nemesis
INSTALLDIR=/C:/Documents and Settings/pandemic/Desktop/gr/jnemesis-1.0-jar
QUEUESAVE=/C:/Documents and Settings/pandemic/Desktop/jnemesis
QUEUESHELL=/bin/sh

The most important thing here is that we are using "/" rather than "\" to seperate directories.

NEMESIS should point to the folder containing the nemesis executable.
INSTALLDIR would be the location of where the extracted folder jnemesis-1.0-jar folder is.
QUEUESAVE should be set to the folder you want to save the nemesis scripts too
QUEUESHELL should be set to any valid unix/linux shell.

After modifying the file as desired copy it to your windows home directory:

C:\Documents and Settings\USERNAME

be sure to rename jnemesis.config to .jnemesis 

To launch the application you can usually just double click on the jnemesis.jar.
However, certain Archive utilities such as WinZIP sometimes look for the extension and think you want to extract the .jar file instead.  Then you will need to start it by opening up a dos prompt and typing:

C:\path\2\java -jar C:\path\2\jnemesis.jar