Unfortunately, the N64 also changed the face of emulation. On January 28, 1999, Realityman released UltraHLE, the first emulator to run N64 games. A couple hours later, he pulled it off of his site, but it was too late. Emulation had turned from reviving old classics to GiMmE Da ®0mz DoOdZ!!! where some games were being emulated within a week after they had been released. It also got Nintendo more involved in anti-emulation activities. However you look at it, whether good or bad, the N64 is now dead, and emulation has progressed quite nicely.
Project64 is hands down the best N64 emulator currently out there. After an almost 3-year hiatus, it's come back strong. The emulator uses Zilmar's plug-in spec, which means you have different plug-ins available for video, audio, and joystick input. Check out NG Emu for the most current plugins.
And, if you're using an Adaptoid, then you're getting the full experience
What's an Adaptoid?? It is the coolest little adapter ever made. It lets you hook up a real N64 controller to your PC and use it as any other joystick that supports DirectInput. Just plug it in and go. No extra software necessary, usually. If you happen to have a program or emulator that only supports the keyboard, you download the driver from Wishtech's site and install it. It comes with a keymapper utility which let's you map any key on your keyboard to any button on your controller. Best $30 bucks I ever spent.