Two of the best games the N64 ever had, and definitely two of my favourite games on any console.
I liked various features of Perfect Dark, like the secondary functions of weapons and the Counter-Operative mode. It also seemed like a much smoother game than Goldeneye. On the other hand, Goldeneye itself was awesome and the multiplayer mode in particular was extremely fun.
I find it quite hard to pick one over the other, but I suppose I tend to go with Goldeneye as I played it more, however if I manage to get my mits on an N64 with both games, I'll be sure to compare them more than I did last time I had the console.