A lot of fans agree that Oracle isn't canon, in part because Capcom produced it and in part because it doesn't make any damned sense with regards to the rest of the timeline. In fact, one could make an argument that the entire Four Swords mythology isn't canon, but is rather some alternate universe/what-if scenario. That would be too bad, though, because there is some good potential with the Four Sword.
As for TWW, we don't know that the water ever recedes. Judging from LttP, OoT is the first game, because OoT comprises the backstory to LttP (seven sages seal Ganon, etc.) The most likely scenario is that after TWW, Link and Tetra traveled off to some new land and founded a new government named Hyrule, which is where the originals take place. We'll find out for sure when TP comes out, since it's slated to take place a few decades after TWW according to Aonuma. TWW cannot come before LttP, because at the end of OoT the Triforce was still split, whereas in LttP it's whole again. However, if Ganon truly had possession of the entire Triforce, he would have been unstoppable; it therefore follows that the pyramid in LttP is, rather than Ganon's fortress, a prison for him, from which he reached out with Agahnim to remake the world and gain enough power to break the seal on the Triforce. This fits with the imprisonment scheme set forth in the LttP backstory.
The general fan assumption is that Link was searching for Navi rather than Saria, because Navi did disappear in OoT's ending. I just wonder how that "encounter" between Link and Zelda turned out...here's hoping they used a condom.
I suppose tangling with the Zelda timeline in a sense prepared me to handle Chrono; it was because of my interest in Zelda that I was turned on to CT in the first place.
