Having James Bond in a game doesn't necessarily make a game better than others in it's genre.. EA has proven that time and time again..
However, when it comes to GoldenEye or Perfect Dark, I'd say GoldenEye was better overall. When you think of Rareware FPS games, you think of GoldenEye. It was the classic party game (much like Halo became for last generation's consoles). PD came out too late in N64's lifetime for it to have time to become a classic. Don't get me wrong, I like it almost as much as GoldenEye, but overall GoldenEye was a better game.
Multiplayer vs. Multiplayer, PD wins. GE paved the way for split screen FPS multiplayer games, but it was ahead of it's time, and wasn't able to do as much as newer games could. PD had much better maps and the bots really helped make it a much better overall experience. Once PD came out, I rarely played GE's multiplayer anymore (no pun intended).
Single player vs. Single player, GE wins. It is one of the only games based on a movie that became a household game title. You rarely see that level of gameplay anymore. I loved PD's multiplayer, but GE is really where the objective based FPS was introduced, and is also the reason PD did so well. When you think of GE, you think of memories of a new experience. When you think of PD, you think of more of the same with a new story. That's not a bad thing, but if I'm going to give one of the games credit as the better overall game, it has to be GE.