I finally found a tool to let me replicate what I saw in a YT video, with PIP (picture-in-picture)-style multiple windows. You can do always-on-top, borderless, and transparency. Only works on Vista and later.
https://ontopreplica.codeplex.com/
One caveat: At least for FFXI windows, I had to leave them "restored" (not minimized). Otherwise they just showed how the game window looked before minimizing.
(Hope it was OK posting here instead of Development > Tools.)