Answer
Simplicity Commander is a utility that provides GUI and command line access to the debug features of an EFM32 device. It allows you to flash firmware, update the kit firmware, and lock, or unlock debug access. This tool is intended to replace eACommander.
Standalone Installation
As of 7/2017, Simplicity Commander is now available as a standalone utility (in addition to the Simplicity Studio-based install/launch options listed below). See the download links listed under the "In-System Programming" section at Production Programming Options for Silicon Labs Devices. Installers and release notes are available for Windows, Mac, and Linux. Please download the installer for different platform here:
installer for windows, installer for MAC, installer for Linux.
See the included README.txt for additional guidance and dependencies (Commander currently requires the SEGGER J-Link software pack to be installed).
Simplicity Studio v3
In SSv3, if wireless support is installed, Simplicity Commander will be available from the "File->Simplicity Commander" menu in the IDE. It will also be installed in C:\SiliconLabs\SimplicityStudio\v3_3\bgtool\commander (depending on your Studio install path). It will also be available, along with a reference guide at C:\SiliconLabs\SimplicityStudio\v3_3\SimplicityCommander
Simplicity Studio v4
In SSv4 the commander binary can be run by going to Preferences->Simplicity Studio->Adapter Packs, selecting Simplicity Commander->commander: commander.exe and clicking on "Bare run". See picture. The binary can also be run directly from C:\SiliconLabs\SimplicityStudio\v4\developer\adapter_packs\commander\commander.exe

Update 09/2017:
In SSv4, Simplicity Commander can be opened from the Launcher perspective. Click the wrench icon near the top left corner, then select Simplicity Commander.

Simplicity Commander
Question
What is Simplicity Commander and how can I use it?
Answer
Simplicity Commander is a utility that provides GUI and command line access to the debug features of an EFM32 device. It allows you to flash firmware, update the kit firmware, and lock, or unlock debug access. This tool is intended to replace eACommander.
Standalone Installation
As of 7/2017, Simplicity Commander is now available as a standalone utility (in addition to the Simplicity Studio-based install/launch options listed below). See the download links listed under the "In-System Programming" section at Production Programming Options for Silicon Labs Devices. Installers and release notes are available for Windows, Mac, and Linux. Please download the installer for different platform here:
installer for windows, installer for MAC, installer for Linux.
See the included README.txt for additional guidance and dependencies (Commander currently requires the SEGGER J-Link software pack to be installed).
Simplicity Studio v3
In SSv3, if wireless support is installed, Simplicity Commander will be available from the "File->Simplicity Commander" menu in the IDE. It will also be installed in C:\SiliconLabs\SimplicityStudio\v3_3\bgtool\commander (depending on your Studio install path). It will also be available, along with a reference guide at C:\SiliconLabs\SimplicityStudio\v3_3\SimplicityCommander
Simplicity Studio v4
In SSv4 the commander binary can be run by going to Preferences->Simplicity Studio->Adapter Packs, selecting Simplicity Commander->commander: commander.exe and clicking on "Bare run". See picture. The binary can also be run directly from C:\SiliconLabs\SimplicityStudio\v4\developer\adapter_packs\commander\commander.exe
Update 09/2017:
In SSv4, Simplicity Commander can be opened from the Launcher perspective. Click the wrench icon near the top left corner, then select Simplicity Commander.
I have the installed wireless support and have no such menu item. How to add it?