I know this has been a while, but I have tried this night to get this to work and for some reason I just can't.
It will do wide screen in v1.6 (can't get it to that in v1.7). But when I do full screen it just goes black for a second and then goes to my desktop (though I can still hear sound).
What's going on? Didn't it work fine for you out of the box?
I can confirm it still works for me on v1.6. You have to do some minor tweaking to the Project 64 settings. At the top, click in the options tab, and then click the option "Configure Graphics Plugin." At the bottom of the box that pops up there is a checkbox that says "Hide Advanced Settings." Make sure that his checkbox is UNCHECKED. Once you uncheck this box, the top of this box should have another tab that says "Advanced." Click in this tab and check the box that says "Adjust game aspect ratio to match yours." Then click back to the "Settings" tab at the top of the box and select the Full Screen resolution that you desire, as well as adjust the anisotropic filtering/anti-aliasing as you see fit (I have them maxed out with my 5870.) Once you do this, click apply, then ok. Now open up Legend of Zelda. It will open up in a small window at first, but press Alt+Enter, and Voila, multi-monitor Zelda. This trick also works for a few other N64 titles, however many have problems rendering correctly. Ones that have worked pretty well for me include:
Legend of Zelda: Ocarina of Time
Legend of Zelda: Majora's Mask
Legend of Zelda: Master Quest
Super Mario 64
Star Fox 64
Mario Kart
Bomberman 64
Donkey Kong 64
Wave Race 64
None of these worked flawlessly, but none were horrible either. There were some ones out there that reallllllllly didn't work with eyefinity, such as Goldeneye or Shadow of the Empire.