In the first Higurashi visual novel, Onikakushi, after the main story there is an extra section where the character are talking about who they think is causing the murders. When wondering why Keichi isn't there with them, Rika explains "he doesn't have a character picture."
In the first case of Apollo Justice: Ace Attorney, Apollo lets out a very loud "OBJECTION!", and promptly gets scolded by the judge and his mentor Kristoph: "Excess yelling can damage the judge's ears... and our case."
You also have Apollo bemoaning how odd all of his clients are and Phoenix making a comment about "presenting" when you try to show him things. Interestingly, characters questioning the trappings of their world is actually a major plot point, as the absurdly unfair justice system which Phoenix previously accepted is now recognized by the characters as in need of change, and that change begins to occur in the final case, with the reintroduction of juries, though admittedly for one case on a test basis.
Ema Skye: "Why can't we have a normal, straightforward killing once in a while in this country?
Ace Attorney Investigations: Miles Edgeworth features a point in the final case in which, just as the true Big Bad looks like he's won, some one shouts out "HOLD IT!". After some dramatic close ups of everyone's shock faces and a tense silence as you wait to see who the Big Damn Hero is, it turns out that the one who saved the day is!...Some random forensic officer who has no name, profile or any relevance to anything at all...