CEN64 is a cycle accurate Nintendo 64 emulator.
Keep in mind this is a WIP (Work in Progress).
At present it has low compatibility. It also requires at least a dual core 64bit processor that has SSE3 support.

CEN64 is a command line program and also requires a PIF image (pifdata.bin) - can be found in MESS N64 rom/bios file.
Presently supports keyboard only.
N64 Roms must be in native big-endian (z64) format.

Usage example:

cen64 pifdata.bin "Legend of Zelda, The - Ocarina of Time.z64"

Several frontends can be found here.