For SNES, there's Higan
https://byuu.org/emulation/higan/It's damn-near circuit accurate, and I'd be scared to question the author why...
For Genesis, I have heard that Exodus is the best. I've played through many Genesis and SCD games on both early emulators and real hardware. I've never had problems with Kega Fusion, tho I hear that I'm wrong by enjoying it's emulation deficiencies.
Having never had a real SMS, I can't fault any emulator, tho having owned a flashcart which had a YM2413 FM chip on board, I can vouch for KEGA having accurate FM synth filtering, and doing better at emulating the sound than a few official releases of the game at the time. Probably, they've done better by now.
NES emulation issues are not as prevalent as emulation fixes. NES games are horribly badly programed, and by default, the emulators give the option to include those bad bugs in your enjoyment of the game with a few checkmarks. I've had many flash carts with everyone's best attempts to make all the games run.
No matter what, you're better off with even 10 years ago's best emulator. It's so much easier to make your computer or handheld play all the games than the real thing.
Here's an old post from long ago on another forum:
http://www.neogaf.com/forum/showthread.php?p=53973564It's no longer accurate.
Probably you should build a device that can do Retroarch.
Just like N64 emulation, only many adopters can iron out small bugs and make everything conform to a single standard. All will soon be devoured by it's bland, unintuitive gray non-interface. Console emulation issues? Why not conform to MESS. "You can throw cycles at it with a multi-core CPU and get cycle-accurate emulation!" 10 years later.
Honestly tho, There's a select few issues with a handful of games that would make those few games interfere with you experiencing the game perfectly through your device of choice.
I'm now dealing with some weird emulation quirks that happen during some Sega Genesis games, where they change their video resolution mid-game. With so many better-interfaced emulators, which can properly handle the mode-change while outputting the video to a 15khz RGB screen.
That's my main goal; Making games output through VGA a proper 15Khz signal on old video-cards so the emulation is undetectable output-wise through any old CRT television...
Finding emulators tweaked to deal with those funky display modes is a bit of a challenge. So-far I haven't had to hack or force any program to function with 15kh screen modes, but I will modify these programs if I have to to get the performance and modes that are required...
), presents a beautiful image, and is very accurate from my experience. 
