OK I am back from class so here is an observation I've made with respect to how Dracula is handled in the Castlevania series.
In the early days, both the players and the games were younger and things like "coherent timelines" weren't really needed. There weren't any really big conflicts, either; Zelda II surely had to have taken place after Zelda I and so forth. Programmers didn't have much space available for setting up long dialogues or complicated cut scenes, and what games did display large amounts of plot did not display expensive translation efforts.
Then, somewhere towards the late SNES era, sprawling plotlines were available and developers had to do a little better than they had before. Games that were obviously not related (like the Final Fantasy series) had no troubles, but working a new Zelda in took some work (it was explained that this Link was one of the original Link's ancestors, I believe). Still, it wasn't until the N64 era that troublesome timelines started to creep in.
Castlevania has handled the issue of Dracula's multiple resurrections quite well, in my opinion, and I think this theory is workable for the Zelda series. The recent CV games Dawn of Sorrow (and the one that came before it that I sadly have never played) depict a post-1999 world where Dracula has been truly destroyed, yet attempts to raise the Dark Lord in a new body are underway. The game's explanation is that with no being of evil, it is impossible for good to exist. When the world lacks evil, the Dark Lord is incarnated in Dracula's form. When Dracula is finally defeated, the Dark Lord has to find a new vessel.
This explains why Dracula always comes back, and even when his body is destroyed his influence still has power. I think Ganon and Link have a relationship similar to Dracula and the Belmonts. Even if Link is able to totally destroy Ganon, the absence of a truly evil presence causes the world to eventually reincarnate him. If no Hero is around to fight Ganon, the world selects a Hero to balance good and evil. The Hero defeats/destroys Ganon, and the cycle begins again.
*edit* Wait... "12 year old brain" "I'm drunk right now" 