There's a new section in the reference section here on 6502.org which lists some 6502 emulation cores for popular microcontrollers. I'm sure there are some missing. I'm not quite sure exactly what the qualifying properties of an emulator should be for this list - ideally it is complete, passes some tests, and the source is available. If there's an appropriate discussion thread it's good to link to it.
See
http://6502.org/tools/emu/#embeddedSome more I am aware of:
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Juan J. Martínez' DAN64 on Arduino[1]/ATmega328
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Darryl Biggar and Eric Ball's NES emulator for Parallax Propeller
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Thomas Giesel's open1541 for XMOS' Xcore.
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Fredrik Petrini's SID emulator for XMOS' Xcore
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Peter Schranz's Apple IIplus on AVR's ATmega1284P
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Jan Ostman's Arduino Nano (ATmega328) VIC-20
Any more? I'm sure there are.
Added:
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Stian Soreng's Apple IIe on ATmega128 with 64K (2x32K AS7C256) external SRAM (No source available yet)
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Vladimir Georgiev's on ATmega328P
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retroelec42's on ATMega162

[1] Arduino uses a particular ATmega chip from AVR, and I'm not quite sure what terminology is most helpful.