My considered opinion is that it beats the hell out of me. If I'm remembering the details you're playing SH4 on a Nintendo 64 with an Apple/MAC emulator displayed on a projection TV using a 1958 Japanese Transistor Pocket Radio for a speaker?
Seriously, my computer is 8 years old, a DELL XPS-400 that originally came with a Sigmatel chip on the motherboard instead of a real sound card. I had so much trouble with that lame thing recording and playing back I finally disabled it in the ROM BIOS and bought a real sound card. On my system the videos sound pretty much the same as what I'm hearing in game.
IIRC you said you have VISTA

which is probably different from XP, but check this;
To see if your sound sliders are all the same - for example the game might be using WAVE while you're hearing youtube on MIDI, if one slider is high and the other low you would get that effect.