I think the answer can be found in the title itself: The Great Gatsby. (Bold added for emphasis.) The narrator is clearly biased in favor of his friend, and we have to assume that this influences the story he tells. Even in his judgments of Gatsby, Nick considers the way his friend is exempt from many of the ways he would judge others more harshly:
Only Gatsby, the man who gives his name to this book, was exempt from my reaction—Gatsby who represented everything for which I have an unaffected scorn. (Chapter 1)
That said, Nick really seems to make a good effort to present the events truthfully and to avoid commentary on the characters' actions to a great extent. He doesn't spend much time judging the extramarital affairs which surround him, and he doesn't comment much on the lack of morality in many of the situations he is placed in.
Yet there are times when we feel the heavy hand of Nick's narration, such as this passage describing the moments just before Gatsby's death:
I have an idea that Gatsby himself didn’t believe it would come and perhaps he no longer cared. If that was true he must have felt that he had lost the old warm world, paid a high price for living too long with a single dream. He must have looked up at an unfamiliar sky through frightening leaves and shivered as he found what a grotesque thing a rose is and how raw the sunlight was upon the scarcely created grass. A new world, material without being real, where poor ghosts, breathing dreams like air, drifted fortuitously about... (Chapter 8)
The important note here is that Nick wasn't there in Gatsby's final moments. He has no idea what Gatsby's final thoughts were, but this narration directly influences Gatsby's characterization. Because Nick thinks of Gatsby as "great," he wants readers to think of him the same.
At the end of chapter 3, Nick tells us, "I am one of the few honest people I have ever known," which is a statement in itself that throws a red flag. Is he really all that honest? He doesn't especially care for Tom or Daisy, yet he continues spending time with them. He helps Gatsby orchestrate an affair with Daisy, a married woman. And he also knows the truth about Myrtle's death—but doesn't rush to the police with the information.
In short, Nick makes an attempt to present the story as honestly as possible, but he brings his own biases to the story, and those influence the story he tells.