There were 3 systems, all with interesting differences.

The original NaCl was a 'validated subset' of native CPU machine code (e.g. actual x86 machine code with some instructions and instruction sequences disallowed which would allow to escape the sandbox).

The next iteration was P(ortable)-NaCl which replaced the native machine code with a subset of LLVM bitcode, which was then compiled at load time. Unfortunately with this step NaCl lost most of its advantages. Startup time was atrocious because it was basically the second half of the LLVM compilation pipeline (from LLVM-IR to machine code). LLVM-IR also isn't actually great as CPU-agnostic bytecode.

WASM was designed from the ground up as CPU agnostic bytecode that's also much easier and faster to validate.

The only major advantage of PNaCl vs early WASM was that PNaCl supported shared-memory threading right from the start (this is still knee-capped in WASM because of the COOP/COEP response header requirement).

...apart from Emscripten => asm.js => WASM, and Google's NaCl/PNaCl there was also a system by Adobe (Flascc/Alchemy(?) I forgot all the names this went through) to compile C and C++ code into Adobe Flash bytecode.

I have an ancient blogpost from 2012 which compares the three (and where I have been flabbergasted by how well Emscripten actually worked - and this was even before asm.js - the linked demo is unfortunately no longer up):

https://floooh.github.io/2012/10/23/mea-culpa.html