With this Autohotkey script, any window can be made click-through, stay-on-top and semi-transparent (transparency level can be changed or set to fully opaque); the default hotkey to toggle transparent/regular state is Win+W.
Please note that it still won't allow you to draw things on top of exclusive fullscreen applications, they need to be windowed or borderless. OBS' display capture will see the "overlays", window capture and game capture won't.
How it looks: (opened a Firefox window with Twitch chat popout on top of S.T.A.L.K.E.R.: Clear Sky)
Regarding the VirusTotal detections ratio: some A/V software blocks all AutoHotkey executables indiscriminately; you can audit and compile the code yourself from the .ahk file, the executable is provided for convenience. Visit https://www.autohotkey.com/
Please note that it still won't allow you to draw things on top of exclusive fullscreen applications, they need to be windowed or borderless. OBS' display capture will see the "overlays", window capture and game capture won't.
How it looks: (opened a Firefox window with Twitch chat popout on top of S.T.A.L.K.E.R.: Clear Sky)
Regarding the VirusTotal detections ratio: some A/V software blocks all AutoHotkey executables indiscriminately; you can audit and compile the code yourself from the .ahk file, the executable is provided for convenience. Visit https://www.autohotkey.com/