If anyone happens to be asking, how does one change this in Portal (Enterprise GIS)...
You can change to custom so that any Web Apps built in Portal will reflect the new icon.
To make the changes in Portal: (2d and 3d viewer app types)
Browse to the Portal Install directory (each Portal if HA)
[portal install directory]\apps\webappviewer\images
Rename the shortcut.ico to shortcut_ORIG.ico
Add your favorite ico that youd like to be used in all web app 2d viewers and name it shortcut.ico
You can make the changes for 3d viewers as well.
[portal install directory]\apps\webappviewer3D\images