AFAIK back in the 90s there was some (proprietary, i think) Motif based program that looked very similar to Program Manager and some Linux distributions bundled it.
It'd be trivial to make something like it with -e.g.- Lazarus, especially if the subwindows/MDI part isn't needed and instead launch toplevel windows (which IMO is a better idea anyway as you can nest them, something i always felt was missing from the Win3.x Program Manager).
EDIT: for fun i tried to setup a Win3.1 theme for Gtk and put Lazarus (in a separate user account) with this window manager. It looks nice[0] though the WM seems to be lacking support for some common features for setting up window appearance (e.g. the completion window in the screenshot has a frame when it shouldn't and the window doesn't disappear but instead its contents become black - this happens for any window that is expected to remain around but hidden).