Or maybe a partial fingerprint from the jilted lover on a can of Diet Coke found in a room of a house she claims she was never in. Dialogue can be a clue. That woman who says she was never in that house provides a clue. The man who says he never, ever wore such ugly shoes or never, ever hit his wife provides a clue. Whether it's an accurate clue or not is another matter.
Relationships can be a clue.
You might think all these are relatively easy, and you'd be right. What's hard is determining when to reveal them to the reader. You see, just like everything else in your story, presentation means everything. In Scott Turow's Presumed Innocent , for example, the clues are a dead woman, a glass with fingerprints on it, semen, and the fact that the main character, Rusty, was having an affair with the deceased. We know about his career aspirations, his fears, the pain in his marriage, everything.