Branching storyline games are a rare breed. They aren't exactly non-linear like the Fallouts, Skyrims, and Mass Effects of the world. Nor are they entirely open world like Grand Theft Auto or Dead Rising. They are essentially a railroaded story, but with switches. Instead of having lots of customizable variables in the universe that determine your storyline, branching storyline games merely give you a choice of paths to take. As a result, developers tend to maintain more storyline control in these games while still giving the player an illusion of choice. Branching storyline games are going out of style, with more open, non-linear games like Deus Ex: Human Revolution taking their place. So let's take a moment to remember some of the best branching storyline games out there with this list.
A little-known PS2 game called Ar tonelico II: Melody of Metafalica featured singing mage girls on top of an artificial helicopter world attempting to wake an ancient machine goddess. Okay, this game's plot was a bit messed up. However, what was interesting was the branching storyline system which sent you down a relationship path with one of three females in your party. Not only did this totally change the story you'd experience and make certain levels of the game completely inaccessible, it also affected your stats directly. The girls that you weren't in a relationship with could not learn magic past a certain point, whereas the one you chose to be your significant other was able to learn the most powerful spells in the game. It was weird, and more than a little creepy, but still cool nonetheless.
In Legend of Mana, the sequel to Secret of Mana, you were tasked with building the world as you traveled through it. Depending on the order and placement of the pieces of this fantasy universe, certain characters and quests became unavailable to interact with. Endings varied wildly depending on what elements were present in what areas of the world you built. The story was never the same twice, yet you always knew where your stories diverged on subsequent playthroughs. This was the coolest part of Legend of Mana (aside from the ability to bring your character over to other players' games in a sort of mail-order MMO way.)
SaGa Frontier wasn't the best-received RPG of the PSOne era, but it had one of the most interesting systems for branching storylines. Right from the beginning, you were given several different characters to play, each with their own story that was wildly unrelated to the others. As the game continued onward, the characters crossed paths and you finally got to see a story begin to develop. However, the order in which you played these character's stories affected the overall storyline of the game. If you weren't careful, entire story arcs would change or become unavailable. Even worse, if you played the characters in a particularly bad order, you may have found yourself hopelessly under-leveled and unable to even complete the game.
All of the Mega10 games contain elements of the branching storyline formula, but Devil Survivor refined the system. This tactical DS game asked you not only to manage what you did, but also when you did it. You had seven days left to live, and you had to choose what to do in every hour of every day. If you weren't in the right place at the right time, important characters could die or go missing. There were numerous endings, and each time you got one you would get a bonus for a subsequent playthrough with an even higher increased difficulty. It almost made it feel like twelve games in one.
Valkyrie Profile had a branching storyline that didn't really give you a choice. The characters available to recruit were randomly generated each time you played the game, and your story differed depending on who was in your party. To unlock the "true" ending, you needed to have the exact right mix of characters, and this required lots of saving and reloading in order to get the right chapters to unlock. However, if you were less interested in playing the game perfectly, Valkyrie Profile was an interesting RPG that had a different story every time you played through it.