EmuNations

Mesen is a high-accuracy NES and Famicom emulator and NSF player for Windows and Linux. 

Features

• Extra High Accuracy: A lot of effort has gone into making Mesen as accurate as possible.

• Extra High Compatibility: Over 290 mappers supported (all licensed games supported)

• NES, Famicom, Famicom Disk System, Dendy, VS System, NSF and NSFe emulation is supported.

• General: Save States, Rewinding, Movie/Audio Recording, Overclocking, Cheat Codes.

• Video: Numerous video filters, customizable palettes/overscan, support for HDNes' HD packs.

• Audio: Stereo effects, per-channel volume and panning, equalizer, etc.

• Misc: Netplay, 7z/zip support, IPS/BPS patch support, automatic updates, and more!

It's currently archived (discontinued), but there are quite a few forks (in no specific order)

• Mesen-X by NovaSquirrel (different fork merges)

• Mesen by webgeek1234

• Mesen by mkwong98

• Mesen by Dwedit

• Mesen by libretro

Fceux is an open-source Nintendo Entertainment System and Family Computer Disk System emulator. It's a merger of various forks of FCE Ultra. While not being cycle-accurate, it's has quite an accurate emulation and offers extensive tools for debugging, rom-hacking, map making, Tool-assisted movies, and Lua scripting.

Nestopia UE (Undead Edition) is a fork of the original Nestopia, but with several enhancements and bug fixes. While being less ressource intensive than others, it still has great accuracy. That said, it does include support for multiple platforms, save states, movie maker, rewinder and much more..!

Ares was originally Near/Byuu's last project and was subsequently continued by new developers (including Luke from Cxbx-r). That said, it's an open-source, multi-system emulator focusing mainly on accuracy and some of its exhaustive features include but are not limited to native multi-platform UI adaptive sync, dynamic rate control, save states, run-ahead, rewind or fast-forward and much more..!

Mesen core (Accuracy)

Nestopia UE core (Balanced)

FCEUmm core (Performance)

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RetroArch is a frontend for libretro emulator cores, game engines and even media players. It enables you to run classic games using Libretro on a wide range of computers and consoles through its unified graphical interface. Settings are also unified so configuration can be done once and applied and applied to all. It has advanced features like shaders, netplay, rewinding, next-frame response times, and more.

It can run on the usual platforms like Windows, Mac OS X and Linux, but it stands alone in that it can support far more platforms beyond just that.

• Ludo - A smaller libretro front end by only implementing the core features and by targeting less platforms but definitely shares a lot of the same core values.

• Lakka - lightweight Linux distribution for small computers like Raspberry Pi

• RArch - It incorporates Kaillera to offer the possibility to play games online. 

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. In addition to its high accuracy, puNES also has some decent, standard emu options, including a input configuration UI.

Nintaco is a cycle-accurate Nintendo Entertainment System (NES) / Famicom emulator and NES Sound Format (NSF) player written in Java, ostensibly making it cross-platform. It supports the vast majority of games including those for the Famicom Disk System (FDS), Dendy, VS. UniSystem, VS. DualSystem and PlayChoice-10, along with a plethora of peripherals. It tracks play history, enabling the player to rewind time to undo mistakes, and to watch, export, edit and resume play at any point in the past. It supports netplay, save states, video and audio recording, video filters, screenshots, cheat codes, a debugger and a TAS editor. It can be controlled programmatically via an API. It provides automatic capturing of sprites and level maps. It even simulates R.O.B., the Robotic Operating Buddy.

Nin is a Nintendo Entertainement System / Famicom emulator that is in the early stages but is actively being developped. 

It's not very polished on the UX side, but can run many games without issues and has gamepad support. 

The exact mapping will depend on the vendor's layout. On a keyboard, the arrows are mapped to the NES D-Pad, Space is Select, Enter is Start, Z is A and X is B. Multiple controllers or other kinds of controller are not currently supported.

iNes was the 2nd Nintendo Emulator System ever released (1996!) after Pasofami, but was the first to be truly easily usable. It also supports the GameGenie, Family BASIC Keyboard, FDS and the VS-System arcade system. iNES offers several graphic filters and even supports online gaming. It has since been ported to Unix, MacOS, MSDos, Windows, Symbian, PocketPC, etc. 

myNES is a portable, open source, low level NES/Famicom emulator written in C#. The compatibility is quite high, running most games without any bugs. Its aim is to reproduce any hardware quirks that games may rely on without relying on game specific hacks or hash checks (aside from filling in pot holes left behind by the iNES file format).