I think it was very precise in its squareness (still unbeatable in joining and matching elements together with no gaps etc), and also well thought out in being keyboard navigable both iteratively via Tab and by shortcut keys through underlined letters (mnemonics). It also strictly followed the guideline saying that anything that would cause subsequent user interaction (like a file dialog) was indicated with “…” as in “Save” vs “Save as…”

No idea how much of this began in Windows but Windows 3.1 was an OS that had it all and it was very strictly followed in a coherent interface.

Sure, I liked the Windows 9x/NT/2K UI too but 3.x was special to me for being early to be so complete in terms of usability.