Though the game Saints Row:The Third makes plenty of references to other video games,like Dead Rising,Street Fighter,and Kirby,two easter eggs arent readily noticable or found by most people.
First,is a Dead Space reference: On any of the cargo ships around Steelport,if you go to the very back of the ship(behind the tower) you will find a small note stuck to a wall(as well as a dead penguin nailed to the boat,but that can be for a differant post) which is a list of missing ships. One of the ships listed on there is a "USG Ishimura",the spaceship from the first Dead Space game.
http://i.ytimg.com/vi/dTkHNAyd9Fg/mqdefault.jpg
Next is a Max Payne reference: If you walk from east to west from the Heli Assault activity in Henry Steel Mills(if lost,there sohuld be an area of watery ground that'll lead you to it) you will come across a small shed with two Toads parked out front and a sign that reads "Payne's Place:Keep off the mud". Approaching the shed,you will hear the sounds of barking dogs. more or less,the shed is a referance to the video game Max Payne (and sorry,I cant find any pictures of it on the net anywhere,but its there in the game)