Ogre Battle 64 is not just the best third-party Nintendo 64 title. It has to be one of the top five thrid-party titles ever released on any Nintendo console. It is a special title.

I love N64. :)

That list sure thinned out compared to the SNES one didn't it? Somehow, despite all of it's weaknesses, it was my favorite system of that gen. I'm crazily, ( we'll see how crazily when I vote ), going with Turok 2. I found Star Wars was great in short bursts, and aside from the WCW game, I had access to superior versions of everything else.

Turok 2

No doubt in my mind.

Snowboard Kids 2

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I voted for Rayman 2 before reading others posts. I'd go with Harvest Moon 64 in hindsight.

Ogre Battle 64, followed by Harvest Moon and Mystical Ninja Starring Goemon. To be honest, I liked these games more than the vast majority of Rare's games.

Of the listed games, RE2 would be my favorite but I beat the PS1 version long before the N64 version came out. So the Turok games then. 

Probably Rayman 2. It's amazing how weak the N64 3rd party support is compared to the SNES.

The N64 had great games. Best console ever.

As far as third party goes, Shadows of the Empire immediately comes to mind, awesome game, but when I'd look through my games, I wouldn't be surprised if there were other great contenders I can't think of right now.