If you do not need an app anymore installed in your Bench environment, you can just deselect and remove it. You can do this with the Bench Dashboard or you can edit the configuration files yourself and call a command on the shell to deinstall the app.
Overview
Deactivating Apps by Mouse
The easiest way to deactivate an app is to use the Bench Dashboard.
To open it, you can use the shortcut in the Bench root folder
or in the launcher folder.
In the Bench Dashboard open the Setup Window by clicking on the
wrench in the toolbar.
To deactivate an app, which was activated by you explicitly, just uncheck its box in the column Active of the App List. If an app was activated implicitly as a dependency and you still want to deactivate it, you can check its box in the column Deactivated. But be aware, that apps, depending on this deactivated app, propably will not work properly.
To kick-off the deinstallation of apps which are installed, but not activated,
just click the Auto Setup Button 
.
If you also want to remove downloaded app resources, like archives or setup programs, from the download cache, you can use the menu in the Setup Window: Setup → Clean-Up Obsolete Resources.
Deactivating Apps by Keyboard
If you want to automate the app removal process, or just want to know how things work behind the scenes, you can edit the configuration directly.
To deactivate an app, that was activated explicitly,
open the App Activation List config\apps-activated.txt
in you favorite text editor and delete or comment out the line
with the apps ID.
To comment out a line, just preceed it with a #.
If an app was activated implicitly as a dependency and you still
want to deactivate it,
open the App Deactivation List config\apps-deactivated.txt
in you favorite text editor and add a line with the apps ID.
But be aware, that apps, depending on this deactivated app,
propably will not work properly.
If you want to get rid of downloaded app resources to free up disk space,
just locate them in the download cache directory
cache\apps and delete them.
To kick-off the deinstallation of apps which are installed, but not activated,
run the Bench CLI with the setup action.
E.g. if your Bench root folder is C:\bench, then run:
cd C:\bench\auto\bin
.\bench manage setup
If you want more information during the setup process, add --verbose
as flag to the command line: .\bench --verbose manage setup.
See Also
Tech Guides
Reference Docs