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FamiTracker
Looks pretty promising; I just switched from using vNES on my website to using NESBox & I can tell you, speed-wise, they both measure up to each other pretty well. Compatibility-wise, it supports a lot more NES games than vNES' Java applet, to the point that even the creator of vNES migrated to NESBox. The emulator has controller input support via Adobe AIR for Windows & Mac users, but Linux users would either need an older package of Adobe AIR, or need to use Joy2Key if they want to use controllers. It supports playing ROMs straight off of the server, but if the parameters for what ROM to open isn't supplied, it will prompt users to supply their own ROMs to run through the browser (goot for testing out compatibility of games, or for adding to a cloud-based project).
It also does near-native emulation of Super NES & Sega Genesis (albeit with a few games being incompatible due to graphical issues,) as well as Gameboy/GBC/GBA games (which I haven't tested out yet).
I thought I'd post this up here in case there are any game devs interested in seeing a sample of it in action; it could be good for hosting your own games on your sites (especially if you create a sample game with limited levels, so that you can sell your carts or sell full featured ROM downloads).
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