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No faces on characters in SSB, unreadable text in Banjo-Kazooie, stuttering images in Mario Kart… the list goes on. For some reason, N64 emulation has never really be cracked and there will always be small glitches with N64 roms that just come as part of the emulation experience ;)

That said, audio glitches can normally be improved by overclocking the CPU or increasing the video memory allocated.

P.S. Windwaker on the N64? Thought that was a Gamecube release?