EmuNations

Mednaffe is a front-end (GUI) for mednafen emulator and it's written in C. This GUI has all sorts of features and even incorporates an inputter maper. It's available for Linux and Windows.
Bear in mind, it needs to have GTK 3 installed.

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...