Referring to Animals: This is the most common usage. Whether you're talking about pets, zoo animals, or insects, 它们 is the correct pronoun.
Referring to Inanimate Objects: Use 它们 when talking about multiple books, phones, chairs, cars, etc.
Referring to Abstract Concepts: It's also used for ideas, problems, situations, or questions.
Informal vs. Formal: In formal writing, using the correct 他们/她们/它们 is mandatory. In very casual digital chats, some people might use the default pinyin input `tamen`, which often produces 他们, as a lazy catch-all. However, learning to use 它们 correctly demonstrates a better command of the language. Its connotation is entirely neutral.