What is a shoutout? This is a reference to another game or show that someone will get ONLY if they've played that game/seen the show. It's not a blatant cameo, but it's one of those things that, if they're paying attention, people get a kick out of.
For example...
In one building, there may be a penguin doll, using one of the penguin sprites from GS2. When you check it, it says:
"A stuffed penguin doll."
However, the FIRST TIME you check it, it also says:
"Hmm? What's this?!"
"Hero found a Grenade!"
They find an explosive item inside the penguin... anyone who's paying attention will catch the Disgaea reference to Prinnies - the exploding penguins of doom.
Another example:
A guard talking about something they need for an upcoming battle:
"It's hopeless... unless we can find those 108 more recruits, we may be in for some serious trouble..."
Which would be a shout out to Genso Suikoden's 108 stars of destiny.
It shouldn't be too obvious, and it should be something that they find when they go around talking/examining things - meaning, it doesn't appear in the main story. They need to be subtle.