Big-Lipped Alligator Moment: "The Piper at the Gates of Dawn" and "Wayfarers All". Both of them have no direct influence on the main plot — Mole and Ratty going hunting for the lost Portly and encounter Pan, and then Ratty gets a brief case of wanderlust. Hence why the are often Adapted Out.
Ensemble Dark Horse: Toad. He's by far the most popular character and tends to get top billing in just about every adaptation there is.
Summed up by later episodes of the Cosgrove Hall TV series devoting the end credits to Toad's song (with the lyrics taken directly from the book).
Ho Yay: Mole and Water Rat show shades of this. Living together is possibly the least intimate gesture that passes between them. Terry Pratchett commented that "the Mole and the Rat's domestic arrangements are probably acceptable, but only if they come out and talk frankly about them." The Alan Bennett stage version turns the whole scene of Mole's first meeting with Badger into a joke about Rat and Badger both competing to homoerotically hit on Mole, who is too innocent to notice.
Values Dissonance: The Weasels of the Wild Wood are lower-class and therefore bad, while the Riverbankers are middle and upper-class and therefore good. Indeed the final passage states how Toad, Mole, Badger, and Rat enjoy summer walks in the now "tamed" Wild Wood and are greeted with respectful deference by the inhabitants — in other words the lower-classes know their place and wouldn't dare rebel against their "betters", ever again.