FCE Ultra is a follow-up
. It is a NES
It seems it was originally based on iNES's emulator engine, but it has been worked on for more compatibility and accuracy. It was the first Linux NES emulator I've seen that didn't have any strange synchronization problems and sounds were really crisp. FCEU is probably one of the best emulators I've seen for Linux (right up there with ZSNES).
If there's only one bad thing to say about the Linux SDL port, the controls are a bit odd - I was unable to get it to recognize the buttons of my USB pad, much less to make it remember them, so the keyboard remained the only controller alternative. The documentation is also a bit, um... lacking. I wish it'd have configuration/usage menus similar to ZSNES.
Official versions exist for Linux (SVGALIB, SDL) and Windows, and also Pocket PC.