Emulator

Pikmin 2 [GPVE01], Redump-approved MD5: 66F8D886AFA0742CD9901D1BFE3B114F

Numerous similar-sounding low-pitch sounds exhibit distortion on new-zelda-hle that isn't present in LLE or real console. Examples of these include:
-Cavern ambience. This is present in all caverns, in every sublevel; normal sublevel music (when present) is played alongside this. Very noticeably different.
-Poison spouts. The difference here is actually subtle enough that I'm not even completely sure it's broken.
-Cave entrances (for caves you haven't completed yet). I haven't paid much attention to these. Situation should be similar to poison spouts.
-Sublevel entrances (e.g. holes from one cave sublevel to another). Same as above.
-The non-meter sublevel-complete sfx. There's two sound effects that play when you collect all treasures on a sublevel: one that you can easily mistake for cave ambience that plays whether you have the Treasure Meter or not (it sounds like something, uh... winding down?), and another after it made by the Treasure Meter, which is just it turning itself off (there's a little jingle, then a, uh, PWAAOUWAAOUWAAoooouuuuuuuu*sizzle*). The former sfx is broken; if you want to hear it without the second sound effect, either go into a Challenge Mode level or start a new file and go through Emergence Cave on Day 2 and collect every treasure in a sublevel.

In addition, the "Save Complete" sfx (but not the "Saving..." sfx before it, oddly enough) plays at what I'd guess to be half the normal pitch. This may or may not be part of the same issue, as IIRC the old HLE didn't have any noticeable problems with the above sounds but did have issues with this (except it was double the normal pitch). Other sfx the old HLE exhibited issues in (e.g. the bridge-construction/wall-destruction completion jingle, the sound nectar makes when you step in it) sound perfectly fine in new-zelda-hle.

As for the µcode CRC, uh... NZHLE reports 2fcdf1ec, while LLE reports e472d69d. This may or may not be relevant, but it certainly is a bug.

(On the topic of unrelated bugs, there's a bug both present on NZHLE and LLERec (haven't tested OldHLE or LLEInt) where the sfx played when you move the cursor around in the Challenge Mode menu gets quieter after a few seconds of being in the screen. I haven't yet confirmed if this is present on real console or not; expect that soon-ish.)

Numerous relevant files (saves, savestates, comparison audio dumps) available here: https://www.dropbox.com/sh/3yswdjndalvbx2h/AACaC0546DyUtFsK8FY1OC16a?dl=0
All audio dumps were made with real-console DSP dumps, unless Dolphin mistakenly overwrote them any time in the last few years. I haven't checked in a while.

If you bother to use the .gci in there, pick file 2 – it'll drop you in a sublevel of the Dream Den (the de-facto last cave of the game) with a few poison spouts (orange squat cylinders with clouds of red-purple gas clouds around 'em), a sublevel entrance, and the omnipresent cavern ambience. To test the not-yet-complete cave entrance sfx, you'd have to exit the cave (either find a geyser somewhere or Start > L/R over to a certain menu > Give Up and Escape or whatever it is) and travel over to where the Dream Den entrance is in the Wistful Woods (follow the map in the pause menu). To test the sublevel-complete sfx, I'd again either go with a simple Challenge Mode level or Emergence Cave.

I apologize for a) filing this issue so much later than I expected to, and b) making it a wall of rarely-useful text.