Originally Posted by fishkake
I'm not entirely sure I understand you, but I think the answer to your question is that the Application loader is used to reinstall the OS on to the device, after a "Nuke". The desktop manager can be used to change applications, but the AppLoader is for replacing the whole OS. The Application Loader can be run without Desktop Manager.
If I'm completely wrong here, please correct me, I don't want to be spreading inaccurate information. Technically I don't belong here, I've got an XDA now, but I still sell BBs...
Desktop Manager (typically "C:\Program Files\Research In Motion\BlackBerry\DesktopMgr.exe") runs the Application Loader ("C:\Program Files\Common Files\Research In Motion\AppLoader\Loader.exe") to install apps and/or load the OS, and the Application Loader can be run on its own without the Desktop Manager.
If you've installed an updated OS for the connected device, Application Loader automatically detects the newer version and will automatically ask if you if you want to upgrade the OS.
When you download and install an app on your PC, the App Loader saves the loader info, and will allow you to uninstall it. However, if it doesn't know where the Application Loader file (*.alx or *.ali), it won't know how to perform the uninstall, so it won't be listed.
Those applications are typically installed Over The Air (OTA) or on another machine, or you've uninstalled or deleted the installation files. Those applications can be uninstalled by going to Settings --> Options --> Advanced Options --> Applications
. Highlight the application you want to uninstall, click the wheel and select Delete.
Desktop Manager allows you to perform other operations like Backup and Install (not another stand alone app), set up sync options (Intellisync - not another stand alone app), and set up redirector option (not another stand alone app).
The other stand alone app of interest is the BlackBerry Device Manager ("C:\Program Files\Common Files\Research In Motion\RIMDeviceManager\RIMDeviceManager.exe") which can be used to connect your Blackberry to your computer to allow "tethering" and communication over the computer's network connection to the BES (and Internet?).
There is a package available from BlackBerry that installs only the Application Loader, but I don't know the URL for it.