My personal favorite acronym like that definitely goes to AROS (Amiga Research Operating System) that if I remember correctly had to - for legal reasons - change the name. Rather than come up with a completely new name, went with AROS Research Operating System.
Edit: name change was apparently to avoid any trademark issues with the Amiga name.
It’s a cheeky play on “WINdows Emulator” as well as “WINE’s Is Not an Emulator”, but I think for both legal (trademark) and logistical (it really isn’t an emulator) reasons, you’ll never officially see that bit sanctioned
My favorite software acronym is PINCE, the reverse engineering tool that’s similar to Cheat Engine in Winblols, that stands for PINCE Is Not Cheat Engine.