The timeless quality of death
Death is in many ways the clock from the title. For one, it is no respecter of age, since the old, hateful, fat, bigoted judge is spared of death, but a good man in his 40's is taken by Leukemia. In another way, since all men die, good or evil, the clock is "without hands," since it does not spare anyone, so it does not change. It's like a clock that is all the time everywhere.
Injustice and hatred
Judge Fox Clane would likely have painted himself as a conservative and a moral man—after all he thinks himself a judge of the world. But in fact, he allows his soul to be tainted by racism, just because he has a bunch of Confederate currency. But as for Malone the pharmacist, the world doesn't bend to his preferences, and he ends up reckoning for his evil, ironically by quoting Abraham Lincoln himself, much to the town's (and his) confusion.
Chronic illness
The main characters are afflicted by a chronic pain, like the pain of failure that begins the novel when the pharmacist fails med school. Then Leukemia becomes his chronic illness (and his terminal illness). For the Judge, life consists of elderly joint pains under the weight of all his fat. Not to mention his blood problems. His diabetes is a constant illness, as well as the left-over effects of his stroke. Perhaps one way to make sense of this constant attention to chronic illness is that chronic illness is a good metaphor for racism in the south. The Judge himself is plagued by his elderly life, and the town is plagued by his hateful leadership and regression.
