Since I'm used to using Credentials Manager on Windows it seems an obvious place to store usernames and passwords. Alteryx has no native way to access these credentials so I made a custom tool using the Python SDK to retrieve them.
It uses the standard library so doesn't install any extra packages and can access any credential stored in the Generic Credentials section of Windows Credential Manager.
Super easy to use, just add to the canvas, enter the credential name to retrieve and run. The username and password are output in separate columns into the workflow.
Please report any bugs 🐞
Get it from the Alteryx Public Gallery: https://gallery.alteryx.com/#!app/Credentials/5f3ff1160462d715e4d43869
Using the tool:

the saved credential:

Enjoy!
Bob Peers, Consultant, Inviso by Devoteam, https://en.inviso.dk