The best replacement for mupen64 is project64.

The best alternatives to mupen64 are rated as following:
★★★★★  project64
★★★★  sixtyforce
★★  n64oid
★  project 64
★  super n64
★  supern64

Your alternative for mupen64 is not listed? Suggest!
Speaking about mupen64, one probably shouldn't forget about sixaxis.

Other search terms related to mupen64 and their ratings are:
★★★★★ sixaxis
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Google Trends

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mupen64
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