An Aesop: In-Universe, Kelderek decides that the true reason that Shardik came once more was to teach the people to value their children, as they are the greatest treasure they have.
Bears Are Bad News: Shardik, despite being God and all, is not a tame bear. Whenever he inevitably ends up destroying massive amounts of property and mauling people it's interpreted as God's judgment by the Ortelgans.
Good Scars, Evil Scars: Bel-ka-Trazet is horribly disfigured by a number of scars. He had received them from a bear mauling before the start of the book.
God In Bear Form: In the main religion depicted in Shardik, the giant bear is known as the Hand of God, aka his physical power and avatar, and is only one aspect of what the Ortelgans believe to be God.
Karmic Death: Several at the hands of Shardik, but most prominently Genshed.
Legacy Character: The chief priestess of Shardik's cult, the Tuginda, is something of this, as no one outside the cult knows who she used to be, how the successor is chosen, or even if the woman visiting this year is the same Tuginda as last year.
Maybe Magic, Maybe Mundane: It's never quite clear if Shardik is just a bear or not. Indirectly, Kelderek admits at the end that it probably doesn't matter and that he'll never be able to convince anyone that was not there. Though at the end a diplomat from the newly discovered kingdom of Zakalon politely speculates that whatever Shardik accomplished was mere coincidence, nearly every time Shardik attacks someone or rampages it is an incredibly significant event that chases the whole shape of the kingdom. First it rouses Ortelga into action, later it results in the destruction of the army set to protect Bekla and at the end it brings peace between the new Beklan empire and Ikat as well as spreading a new, more benevolent cult of Shardik across the land.
Reincarnation: Shardik is believed to be immortal because of this.
Single-Target Sexuality: Kelderek is well known for his chastity. Women simply do not interest him, both before becoming the priest king, during that period or after. The only woman to whom he expresses any attraction is Melanthys, who deserts her post as priestess quite early in the story.
Survival Mantra: Children in the possession of slave-dealer Genshed tell each other they'll be "home soon. Underground, all the way".
The Unseen: The brilliant southern general, Santil-kč-Erketlis, never appears throughout the whole book, though his actions have a serious impact on the main plot.
You Have Outlived Your Usefulness: Ta-Kominion only needs Kelderek and the Tulgina until he takes Bekla. After that, he figures he'll probably get rid of them quietly and try to reform the cult to surround himself instead. However, a minor wound grossly mishandled causes him to fall deathly ill and he is crushed beneath the wheels of the cart transporting Shardik before anything can come of it.