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). 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.
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. 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. Of course we've all heard of FlashNSF & it's ability to play NSF & NSFe files from a web browser (great for showcasing your tracks from your own website, as seen on MMLShare,) but I found something that looks like it can outdo NESCafé & even the original vNES Java applet NES emulators.