I don't think WebAssembly has been applied across a whole system just yet. Inferno/Limbo (the successor to Plan9, using the Dis virtual machine) may be substantially closer to the mark, along with AOSP (based on Dalvik/ART) and a variety of JavaScript-based "web" OS's. One may also argue that "image"-based systems like Smalltalk, Oberon etc. are in the same class, and that the lineage ultimately originates from Lisp machines.
Smalltalk predates Lisp machines and didn't originally compile to native code at all. I don't remember if Limbo did. Oberon isn't image-based (you can't save and restore the memory state of the running system) and didn't originally define a machine-independent bytecode format, and the one it had for many years has been removed from the current version. Wasm usually isn't image-based either; though it has a clear pathway for doing so, for example Wasmtime still doesn't implement that functionality: https://github.com/bytecodealliance/wasmtime/issues/3017
