In an interview with Official Nintendo Magazine (as transcribed by ZeldaDungeon), Eiji Aonuma commented on the placement of The Legend of Zelda: Skyward Sword in the oft-speculated timeline of the franchise. More notable than the game's positioning was Aonuma's confirmation of an overarching Zelda timeline -- though he explained that it's a "confidential document" to which only "myself, Mr. Miyamoto and the director of the title" have access.
Aonuma revealed that Skyward Sword comes before Ocarina of Time in said timeline, but wouldn't comment on whether it's the first game in the chronological series. He explained, "for us to add titles to the series, we have to have a way of putting the titles before or after each other," hence the secrecy. That makes sense -- as long as they're all comfortable with the swirling, black morass of insanity that's surfaced due to their reticence.