EmuNations

Mednafen is an open-source, multi-system emulator, driven from the command-line, OpenGL and SDL. Its Sony PlayStation, Sega Saturn, Nintendo Virtual Boy, and NEC PC Engine (TurboGrafx-16) original cores are recognized for their high quality...

puNES seems to be ranked as the second most accurate NES/FDS emulator behind Mesen.  Like many other Famicom emulators (such as Nestopia), it has cycle-accurate CPU emulation...

Hades is a recent entry in the GBA emulation, but it has a decent accuracy, speed and features. That said, while it does not have the most features in its category, it still covers the most practical as-in game controller support...