JL_Cmder is a very basic application with no actual user interface to speak of. It is essentially a command line tool that runs off your PC that allows you to perform important tasks in case your phone is bricked or not responding. A couple of keystrokes will allow you to perform each of the applications functions. To use the application you first need to install the RIM BlackBerry Desktop Manager software or BlackBerry USB and Modem Drivers for your phone. They can be downloaded from the Blackberry Website.
The options offered in the tool are -

click to enlarge
deviceinfo - which allows you to view the phone information in a text file
eventlog - that exports your event log to a text file. You could use this to check for problems on your phone.
screenshot - this allows you to take screenshots of your phone screen
wipe - This command will remove the current OS in your device. It is the most useful feature on this application and it allows you to recover your phone from unresolved problems. You could also update your phone OS after performing a wipe command.
resettofactory - This command keeps the OS, but restores the phone to factory settings.
Command-line usage - this allows you to control your device using the command prompt. This is strictly for power users.