Small Gods is one of the less hysterical and more profound of Pratchett's novels. The central theme, reprised from another angle in Hogfather, is belief and its necessity, to both humans, and gods.
In this book, Pratchett examines hypocrisy, providing us with a hierarchy who have no faith in the god that forms the lynchpin of their religion, but are absolutely committed to the trappings of the church and paralysed by their fear of the power wielded, and inevitably abused, by the head of the theocracy, Vorbis.
In the person and development of the character of Brutha he examines the simple, credulous faith of the uneducated and indoctrinated, and shows that constant and widespread questioning and challenge are necessary to mitigate misuse of power (whether by church or temporal government) and enable progress.
One of the most interesting elements of the book is the "Small Gods" of the title. These are beings who once held sway over nations, but have dwindled to shadows as belief in them has died; they can symbolise ideas and scientific tenets as easily as gods or religeous faith. It is to avoid becoming one of them that Om, the god at the centre of the church in the book, clings to Brutha.
The outcome is a man who is able to inspire and lead the country back to faith through his solid certainty in the existence of his god - but a gentler, less proscriptive and more human faith, influenced by the need of the god for its general acceptance, if he's to survive beyond Brutha's lifespan.
Small Gods is held to be one of Pratchett's most accomplished and significant works, and while it doesn't lack humour, the humour within it reinforces the (somewhat cynical) central message.