Several Mystery Series I Unreservedly Recommend

Nate the Great by Marjorie Weinman Sharmat
For the early reader (no chapters), Nate solves crimes using logic children can understand (red and yellow paint mixes to make orange, licking a stamp makes it sticky, etc.). As he goes, he narrates his thoughts, causing the adult to hear mystery music in the background. He leaves notes for his mother, promising to wear his rubbers, and pancakes are his favorite payment.

Three Cousins Detective Club by Elspeth Campbell Murphy
For the elementary reader (early chapter book, slightly easier than American Girl series), each book is told from the perspective of one of three cousins: Sarah-Jane, Timothy, and Titus. The series is explicitly Christian, and there are sub-series themed around the ten commandments, the Beatitudes, etc. The cases and characters interest a young reader, but as an adult, I especially appreciated the emotions that the kids experience. For example, they deal with mixed emotions about younger siblings, they struggle with fixing a bad attitude, and they feel attachment to and embarrassment toward their stuffed animals.

Addie McCormick by Leanne Lucas
A Christian series for the elementary reader, Addie and her friend Nick discover secrets and have adventures in rural Illinois. The characters are well developed and frequently wrestle with how a Christian should respond in the situation.

Sherlock Holmes by Sir Arthur Conan Doyle
The famous mystery series is generally appropriate for the intermediate reader, although the cases are often dark and the villains viciously evil. Also, the student should be able to appreciate the strength of intelligence and observation possessed by Holmes while not condoning his character flaws of pride and addiction. The worldview is humanist. That sounds like a reservation, but if I had confidence in the student's discernment, I would not hesitate to let him read any of the series.

Father Brown Mysteries by G. K. Chesterton
About the same reading difficulty as Doyle's mysteries, but far superior in worldview. The priest solves his mysteries not only by observation, but by an understanding of mankind. His detective thesis might be: every man is capable of great evil, but also can be redeemed from that evil through faith. Brown seeks not only to solve intellectual problems, but to minister to the souls of those involved.

For the advanced reader, I recommend anything by Agatha Christie or Dorothy Sayers.