Perceptions of Time
Much of this story is concerned with how people view time, either as a gift or as a commodity. While working on his painting, Niggle tends to view his time as a resource to which he has rights. He deserves to spend all of his time in the manner he sees fit; things he finds that he has to do, either to stay afloat in the world or to serve others, are irritating strains on this time which he feels to be unjust. While he works in the Workhouse, however, he begins to see time differently: he has no "free time" of his own, yet the time he spends in work is fulfilling, and rest becomes exponentially more complete and fulfilling. By the time the novel ends, and Niggle has gone into the Mountains, time no longer seems to have any meaning; he has completely let go of his tight grip on time, freeing himself to enter the land of the Mountains.
Creation
Evident in this story is Tolkien's theory of "sub-creation": God is inherently creative, and, as we are made in his image, we may reflect this attribute by creating in return, arranging and reorganizing the things that have been made as a sort of worship of God, participating in his divine nature. This pursuit is ultimately worthwhile, and the story reflects this worldview: Niggle spends his whole life attempting to create something beautiful, and in the afterlife, he realizes his creation in the fullest possible sense, giving credence to the world of the imagination.
Imagination vs. Pragmatism
Tolkien is a firm proponent of the value of the imagination, and "Leaf by Niggle" exemplifies this position. Niggle spends his whole life occupied with his imagination, trying to realize in real life the beauty he sees through his imaginative faculties. He is mocked by the rest of society, who don't see the value in what he's doing. Its value, however, is emphatically asserted in Tolkien's representation of the initial stages of the afterlife; when he arrives, Niggle notices that it is the exact form of the things he saw in his imagination, embodied with a realism he couldn't have imagined. This implies that imagination is perhaps somehow more real than the physical world, a curious argument but one with some reasonable support. At the end of the story, this beauty is contrasted with the vulgar, pragmatic materialism of the town council, who notices that Niggle didn't really have much use for society.
