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Well at least for me BigPEmu the Jaguar emulator came out of nowhere and I've read it's pretty good. I don't think there's been much progress on the N64 front, but I think Rosalie's Mupen GUI which is fairly new has become one of the easiest/best ways to emulate N64 these days. And although not a 'system emulator' as such, DREAMM is also a fairly recent project for playing old LucasArts games.
Older than N64: Sardu released an NES transistor-level simulator based on Virtual6502. https://github.com/iaddis/metalnes
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.