I don't think this qualifies as a "guide" but it's something I wanted to write up so people are aware.
I downloaded some VODs and did some frame counting and I noticed two major areas of slowdown for emulators:
The cutscene that plays between Hide and Seek episodes lags really noticeably in emulators, and it seems to cost about 6 seconds per episode. The other cutscenes don't appear to be appreciably slower.
The loading time between levels isn't as noticeable because nothing is happening, but it seems to be about double (!) in the emulator. This varies depending on stage complexity, but it goes from 1.500s to 3.000s for Rescue 1:1 => 1:2 and 2.400s => 5.000s for Rescue 10:9 => Rescue 10:10. If I take a guess that the average level lag is 2 seconds, and there are 100 level loads, that's 200 seconds, or about 3 minutes 20 seconds (!) lost on emulator over the course of the Rescue run.
The other thing I noticed is that FFRPro's Rescue PB plays the "Stage" cutscene (about 1m53s long) after Rescue 5:10, and both mine and RebeccaRE's plays the "Love" cutscene (only about 25s long). I'm curious if there's multiple versions of the game with different cutscene ordering, or something else.
Never played N64 emulator before, but if there's a huge difference, it would be better separating emu from console. We did that in some Resident Evil Leaderboards because there's a lot of difference in load times.
Ok, so with jammitch's analysis of load times between EMU and N64, I have gone the Super Mario 64 route and separated the runs between being done on Nintendo 64 and being done on Emulator.
I've also wondered about if there are indeed different versions of the game out there (1.0, 1.1, etc.).
After posting this, I wanted to check that the issue was "Emulators" and not just "Project64", and I can confirm that other emulators have similar lag. I tested PJ64, along with Mupen64Plus 2.0r in RetroArch (couldn't get the latest version figured out today because no frontend) and ParaLLEl 2.0 in RetroArch. The results are pretty similar.
loading 1.6.1 => 1.6.2 Real - 1.933s PJ64 - 4.233 Mupen - 4.200 ParaLLEl - 4.200
Cutscene Real - 17.334 PJ64 - 26.300 Mupen - 24.333 ParaLLEl - 25.533