When the suspects in Jisei are confined by a detective to the scene of a murder amidst the unknown murderer, Kizaki, who is in a panicked state, exaggerates the situation as a Closed Circle where he could potentially be attacked by the murderer. The protagonist counters that Kizaki has access to the internet to call for help, and insists that the plot is not Ten Little Murder Victims.
From CLANNAD, Kyou gets a moment while trying to convince Kotomi to get Tomoya to walk her home after a dangerous man approached her:
Kyou: Listen. This is an Event Chance. Just tell him, 'I am scared, so I want you to take me home', in a charming voice.
And another talking to Tomoya about his relationship with Ryou:
Kyou: Are you an idiot? Your relationship with her will level up if you secretly buy it as a present later on! If it works well, you might trigger an event flag, then you'll feel really happy.
In Katawa Shoujo, Hanako notices quickly that Hisao, despite his good intentions, approaches her with a rather patronizing attitude and generally acts like she is completely helpless. And if he keeps it up, she will NOT be happy about it.
In Dra Koi the protagonist seems quite aware of how a story runs, but is unaware that he's the protagonist. He still realizes he's falling into a romantic comedy, though.
The third game has a moment where, while investigating a robbery, Maya mentions how she thinks of victims as being dead because they're always on murder cases.
In the fourth game Apollo Justice laments about why all his clients seem to be weird.
Apollo also laments at one point that he wishes he could just have a normal trial.
Kay from Investigations seems to be Genre Savvy on a lot of things, such as main characters having young teenager assistants, groups of three young and bubbly teenager vigilantes and the fact that thieves are supposed to have a certain image to them.
Investigations 2 becomes genre savvy also, although somewhat subtly, by playing around the the fact the series is mostly text. Edgeworth's "objection!" voiceclip is at one point used by someone else, much to Edgeworth's shock, for example.