Application Properties
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By choosing "Properties" after alt clicking on an application, you can change many things about the way the application appears and functions in

By clicking on the icon in the properties dialog, you can change the icon used by for the application

This controls the text displayed by

You can specify the parameters to pass to a given application.

This is another way to specify the category for an application.

Automatically start with
If this is checked, the application will automatically start when is launched

Autorun Profile
If you've defined more than the default profile for an application, this allows you to control which profile is used when the application is automatically started with (see "Automatically start with" above)

Start Application
This allows you to force an application to start minimized or maximized

Add New Profile
You can define multiple "profiles" for an application, which will allow you to launch an application with different parameters.  You define a caption for each profile, and can specify whether the window should start minimized or maximized. 

For example, by specifying the parameter "--incognito" for Google Chrome, you can have it launch in incognito mode, or you could specify the profile to load for Portable Putty.

Each profile you define will appear as an item on the alt-click menu for the application