Mr. Betteredge employs animal metaphors and verbal irony to describe the "wicked Colonel" John Herncastle in Chapter 5 of Period 1, implying to the reader that he is vicious, instinctual, and fierce:
They are very strict in the army, and they were too strict for the Honourable John. He went out to India to see whether they were equally strict there, and to try a little active service. In the matter of bravery (to give him his due), he was a mixture of bull-dog and game-cock, with a dash of the savage. He was at the taking of Seringapatam.
There is a sense of insincere, comedic restraint in Betteredge's descriptions of Colonel Herncastle in this passage. Betteredge calls Herncastle "one of the greatest blackguards that ever lived" just before this. However, he goes on here to refer to him by the sarcastic nickname "Honourable John." Of course, someone who is a "blackguard" is not honorable at all, which is why the verbal irony of this misnomer is so effective. This sarcasm continues in his description of Herncastle's time in India as a way of seeing if "they were equally strict there": the idea that the British Army would be more lenient in some places is an unlikely one.
In saying that the Colonel has "a dash of the savage," Collins uses the metaphor of animals trained to fight to death in betting arenas to characterize Herncastle. "Bull-dogs" and "game-cocks" were chosen for their savagery, and so, he implies, Herncastle is savage by nature.
The word "savage" here is also a pejorative reference to the native Indian population that Herncastle goes to India to try and subdue. The "taking of Serangitapam" was a famously violent suppressive military action by the British in colonial India. As Collins immediately refers to this battle after Betteredge's animal metaphors, it's unclear whether he means the "dash of the savage" he says Colonel Herncastle has in place of "bravery" is an Indian or an animal trait. Given the largely negative depictions of Indian characters in this novel, it seems likely to serve both purposes.
Many scholars have observed that Rachel Verinder is metaphorically aligned with the Moonstone throughout the novel; Rachel "is" the gem in many ways. Both Rachel and the diamond are often discussed as "beautiful" but "flawed," and both have their "worth" explicitly questioned and discussed by those around them. In Period 1, Chapter 6, Mr. Blake Sr. describes a problem which affects the value of the Moonstone:
[...] there was a defect, in the shape of a flaw, in the very heart of the stone. Even with this last serious drawback, however, the lowest of the various estimates given was twenty thousand pounds.
Even though the gem is "flawed," which is a "serious drawback," it's still extremely precious. This discussion immediately follows an observation by Blake Sr. that "the question of accurately valuing it presented some serious difficulties." These "difficulties" set the stage for an extended assessment of Rachel's physical appearance by Mr. Betteredge a little later in the same Period. He describes her as being "one of the prettiest girls your eyes ever looked upon." However, this prettiness is qualified. Rachel is beautiful provided that the "looker" has "no particular prejudice" about any of the many things about her which Betteredge then lists as physical defects or unfashionable traits. Betteredge always aligns Rachel's value with her beauty, as the Moonstone's value is dependent on its appearance.
The stone and Rachel's body are powerfully and repeatedly aligned in the novel, but the Moonstone is also symbolically linked with Rachel's personality. The gem is flawed in its "heart," as characters like Miss Clack and Betteredge believe Rachel to be due to her internal imperfections. These include things like her "straightforwardness" and other characteristics that don't line up with Victorian ideals of femininity.
Finally, the gem also metaphorically represents Rachel's virginity. Virginity was at a premium for unmarried Victorian women, as it wasn't considered socially acceptable to have sex before marriage. Both the Moonstone and Rachel's "virtue" are depicted as precious possessions with monetary value, which need to be protected. When Franklin Blake comes into Rachel's room at night and "steals" the gem, he symbolically "takes" her virtue, and much of the novel's plot involves the search to get it back. What's more, though Blake "steals" the Moonstone from Rachel, he eventually also marries her. By the end of the novel, then, there's still a "diamond" in the Verinder family even though the Moonstone is gone. Rachel's "virtue" (even if it's flawed) is restored to her via her marriage.
Miss Clack uses a hyperbolic biblical allusion in Narrative 1, Chapter 2. This allusion functions as a metaphor to describe some visitors arriving to accompany Rachel Verinder to a flower show. In this section Clack tells the reader that:
[...] a thundering knock at the street door startled us all. I looked through the Window, and saw the World, the Flesh, and the Devil waiting before the house – as typified in a carriage and horses, a powdered footman, and three of the most audaciously dressed women I ever beheld in my life
Drusilla Clack thinks Rachel is arrogant, badly behaved, and un-Christian, and is always trying to improve her behavior by forcing fundamentalist religious pamphlets on her. It's unsurprising, given this, that Clack believes Rachel's friends are "the most audaciously dressed women" she's ever seen. The situation she is describing—people arriving to pick up a friend in a carriage—is actually quite normal, but through Clack's hyperbolic voice, it becomes an occasion of bombastic significance.
Clack refers to the girls in the carriage as "the World, the Flesh, and the Devil waiting before the house." This trio of things is an allusion by the author to the writing of Thomas Aquinas, a 13th century Italian theologian. Aquinas described the three things Clack references here as the "implacable enemies of the soul." Aquinas is a canonical Christian figure, and this reference would have been a familiar one to Collins's largely Christian British audience.
Of course, the idea that some flashily-dressed girls in a carriage could be the embodiments of the "enemies of the soul" is obviously farcically overblown. Nevertheless, Miss Clack sees opportunities for sermonizing everywhere, especially when they involve criticizing Rachel. This is another instance in The Moonstone where the insatiable Miss Clack makes a ludicrously exaggerated and negative religious reference to align something quite ordinary, even pleasant, with something very bad indeed.
Collins describes Rachel Verinder's complicated love for Franklin Blake (which she is implicitly confessing to Godfrey Ablewhite in the passage quoted below) through a paradoxical metaphor. In Chapter 5 of the First Narrative, Miss Clack overhears Rachel ask Godfrey what he would do had he ever loved someone who was "unworthy" of him:
And, suppose, in spite of all that – you couldn’t tear her from your heart? Suppose the feeling she had roused in you (in the time when you believed in her) was not a feeling to be hidden? [...] How can I make a man understand that a feeling which horrifies me at myself, can be a feeling that fascinates me at the same time? It’s the breath of my life, Godfrey, and it’s the poison that kills me – both in one!
Rachel speaks in general terms here, but the reader knows she can only be referring to the painful situation she's facing with Franklin Blake. As she believes he stole the Moonstone, she thinks he is "unworthy" of her, but can't help loving him anyway. When Rachel says the feeling that "horrifies" and "fascinates" her is "the breath of my life" and the "poison that kills me—both in one!" she is using a paradoxical metaphor to explain her confused feelings. The metaphor refers to her simultaneous joy in her love of Franklin and her disgust at what she believes he has done. She is horrified by her love (it "poisons" her) and also sustained by it (it is her "breath," the thing that keeps her going.) This metaphor is paradoxical because these emotions would usually cancel each other out, and yet she feels them simultaneously.