Okay, here's the best picture I could find to explain it...
So, as you can see, the Minish Cap Link is the first, despite not being the first in the series. After he slays Ganon for the first time , presumably at one of his weakest points, one of THAT Link's descendants fights Ganon again, this time while he poses as a human. When he gains the Triforce power, two timelines are created: one in which Ganondorf DOES take over the world (The Adult Link timeline) and one where he is thwarted before ever doing anything (The Young Link timeline). In the Young Link timeline, since Navi had left due to Link not needing a fairy at that point, went after her, and got caught up in the Majora's Mask story. After that, he journeys across the ocean for no presumed reason, gets struck by lightning, goes into a coma, and awakens the Windfish to wake back up. From that point, we see the stories of Zelda 1 and 2, in which Link hones his skills as a swordsman, eventually acquiring the Four Sword and battling Vaati who was actually being controlled by Ganon. Then HIS descendant goes through a similar transformation to Ocarina of Time, except THIS time, there is no time jump, just a jump between dimensions/worlds, and thus no split timeline. Meanwhile, in the Adult timeline, Link's grandson or whatever saves Hyrule again, this time with the help of Midna and defeating Zant in the process. There is no indication that Ganon every actually died in Twilight Princess, so perhaps he regained power after healing from his Master Sword impalement, and then flooded Hyrule. After the events in Phantom Hourglass, the gods realize what great warriors these two Links are, and then Din and Nayru (and Farore, technically) reunite the timelines so they can stop Twinrova from summoning Ganon again and sending all dimensions and universes into oblivion.
WHEW... that took a LOOOOONG time... But it feels good to know there's at least SOME clarity.