Recently I decided to go on a long and epic hunt for references in video games. Many of these may not have been intended as references but I thought they were and will not mind if you correct me. This is the list I have conjured up so far.
GTA 5- In preparation for the FIB heist whilst waiting for the janitor to leave the garage I found on the SAT-NAV on the car that Michael and Lester are in there is a map of Liberty City and Alderney city from GTA 4. This may be the case in every one of these cars or it could just be a model from the previous game. It also features The Republican Space Rangers from its predecessor
Dragon Age: Origins (or just Dragon Age)- In the Deep Roads there is a codex by the name of "Strange Note". This references Bioware's other main series Mass Effect. It says that "the mass is having an effect" and "what kind of dwarf is called Shepard (the player character in the Mass Effect series.)
Saints Row IV. I have found a number of references in this game. First is the title Saints Row IV which is likely a nod to GTA IV because Saints Row has long been considered a GTA clone. They also noted it's cloning reputation by calling Jonny Gat's clone GAT V clone (as in GTA V clone). A creator of the game later said "We wanted to pay homage to the series that gave this genre a name." There are also a number of Bioware references in Saints Row IV notably the Romance option, a feature in all the Mass Effect and Dragon Age games to date. It seemingly mocks it because in this, no-one cares if you have slept with someone else, whereas in Bioware games they bring it up. It also references a conversation between Aveline and Isabela in Dragon Age 2 DLC Hawke's key when Aveline says to Isabela "Break him, and wear pants.", when the leader of the Saints comments on Saints Row 2 Shaundi that He/She says "I always thought she was just a fun girl who didn't wear pants"
Dragon Age 2-Whilst Dragon Age 2 was released after Saints Row 2 but before Saints Row IV this does not mean that the first reference was created by Saints Row. The similarities between Shaundi's appereance and Isabela's are obvious. The fact that Dragon Age made Isabela so similar to Shaundi is probably what caused Saints Row to decide to have a Dragon Age 2 reference. With the release of another Dragon Age in Autumn or Fall depending on where you come from you have to wonder whether the favor will be returned. Another reference I found in Dragon Age 2 was to the first game when Alistair repeats his infamous "Swooping is bad" line