I know one case has The Adventure of the Lion's Mane as a piece of evidence and that Holmes deduces the reason a witness has it because "he really likes lions." Also, last case has Holmes deduction of another witness' plan being basically the plot of The Red-Headed Leage.

TBH, I wonder how much Capcom can get away with if they pulled a Herlock Sholmes and altered the names/references to the Holmes cast and stories.