What smells affect Jay Gatsby ? How and where in the book?
In Chapter 8, Nick describes Gatsby's impressions of Daisy when they were younger and he visited her house:
There was a ripe mystery about it, a hint of bedrooms upstairs more beautiful and cool than other bedrooms, of gay and radiant activities taking place through its corridors and of romances that were not musty and laid away already in lavender but fresh and breathing and redolent of this year’s shining motor cars and of dances whose flowers were scarcely withered.
Gatsby associates freshness with Daisy and with success (thinking financially here). There is a "ripe" mystery (ripe—full of life, blossoming) about Daisy's home and the social circle she has always lived in. Nothing was (or smelled) old, nothing was "musty." There is always something fresh about Daisy (aptly named for a flower), which is redolent (meaning reminiscent or fragrant) of newness, od shiny cars and of course fresh flowers. So, in this quote, there is not a particular smell that affects Gatsby, but he conjures the sense of smell in his idealized memories of Daisy.
Gatsby idealizes and idolizes Daisy like a perfect flower (always fresh and ripe) that never wilts nor fades. When Gatsby leads Daisy into his house, she notices the flowers:
With enchanting murmurs Daisy admired this aspect or that of the feudal silhouette against the sky, admired the gardens, the sparkling odor of jonquils and the frothy odor of hawthorn and plum blossoms and the pale gold odor of kiss-me-at-the-gate.
It is this idea of freshness (the freshness of a dream remembered) that Gatsby associates with Daisy. This is fitting considering the fact that he's remembered her as she was all those years ago. He keeps the dream of her alive in his mind the way he tries to keep the flowers fresh.