This is the metapuzzle, so it will use all of the answers from the nine puzzles. But first, the story text suggests that the suspects Layton has met are important. At the end of the prologue he says "I should start by rounding up the usual suspects," and at the end of this puzzle's story he says "Our suspects proved far more colorful than we imagined."
Looking back at the story in each puzzle, Layton encountered a suspect in six out of the nine locations he visited. Reading the story closely, the identity of the suspects can be gleaned. The story text that appears at the bottom after the puzzles are solved provides much stronger hints than the story at the top. Each suspect is a villainous fictional character that is associated with a particular color. The full list is below, with some of the key clues from the story that can be used to identify the suspect.
|Bar||The Grinch||Story is written in Seussian rhyming style, stole things for Christmas|
|Bookstore||White Witch||Addressed as "Your Majesty", implied to not be human, Layton almost says her series has 7 books, carries a wand that turns people to stone with a Word|
|Country Club||Waluigi||Plays tennis, lots of words that begin with WA/WAL, tall and lanky with overalls and orange shoes|
|Dance Hall||Mystique||Is female but looks like a man, morphs into a raven (Raven is her given name)|
|Gallery||Sinestro||Floats and has a thin pencil mustache, exhibit is about extra-terrestrial life in comic books, implied to not be human, needs to charge a lamp|
|Office||Carmen Sandiego||Wears a wide-brimmed hat, references to world travel and items she's stolen, the word "acme" is mentioned|
The six suspects are green, white, purple, blue, yellow, and red. These are the same six colors associated with the suspects in the board game Clue. This also fits with the fact that Layton is investigating a murder and he's at a mansion.
Layton says he's found something in one of the rooms; the Clue mansion has nine rooms and there are nine puzzles. Each puzzle answer has the same number of letters as a room in Clue, with exactly one overlapping letter. In addition, the puzzle title and answer are both thematically associated with the corresponding Clue room.
Mapping out the answers on the Clue board and reading the overlapping letters clockwise from the bottom spells BODYSALON, so Layton found the BODY in the SALON.