EmuNations

BlastEm aims for cycle accuracy while also hitting lower system requirements than similar emulators. It has substantially higher compatibility than Exodus but falls short of Genesis Plus GX...

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...