In the Fire Sanctuary, several of the Mogmas, after being rescued, say to you "I don't know who you are or where you come from...", a reference to rescuing the carpenters from the Gerudo Fortress in Ocarina of Time. After rescuing each carpenter, they each start off their thanks by saying "I don't know who you are or where you come from, but...".
There's plenty more, but I don't think anyone has mentioned this one yet.
As I played through Skyward sword for the first time, I was so into the game that I just played straight through, not stopping to look at the scenery. When I went back and played it again, I noticed a few things that referenced other games. One was the necklace that the repairman was wearing. I don't know his name, but he's the one who fixes the windmill for you. Anyway, the necklace he was wearing looks just like the "pirates necklace" from Phantom Hourglass and Spirit Tracks. In the phantom hourglass, it was said that "this necklace is worn only by one who is destined to be leader of the pirates." Could this mean something? On a more obvious note, the big tree in the faron woods, could it be the deku tree? We go inside it at one point of the game, and its climbing and ledges do resemble those of the great deku tree we all know and love in oot. So besides the obvious (like the master sword) do you guys see anything else that could relate to other Zelda games? I'm genuinely curious.
I didn't notice anything, and personally I didn't bother to look.
Although, the Great Deku Tree theory could work since this game is a prequel to Ocarina of Time.
As for the pirate necklace, that's simply illogical and has no correlation with SS.
Well I never saw the necklace thing.
That tree I'm sure is not the Great deku tree since it does not speak, unless it becomes enchanted at a later stage.
There is the place where link lays the master sword to rest at the end of SS in the temple. It is likely they built that into the temple of time.
There is also a link skeletal structure in the earth temple which resembles volvagia's bone structure from OOT although it is allot bigger in SS.
I too have also seen some refrences to other Zelda games while playing Skyward Sword. When you break a boulder while swimming in Faron Woods, a Parella will say "It is a secret to everyobody" whic is a famous Quote from the original Legend of Zelda. Farore's mark is also on the stone door, as well as the Healing pot in Lake Floria. Din, Farore and Nayru are also mentioned frequently throughout the game.
The biggest refrence, however, is at the very end of the game.
When the Godess Statue is brought down to the Earth Below, it connects with the Sealed Temple. When you begin to walk out of the newly-connected Temple you will go through a dome-like section. If you look up at this section you will see all of the Medallions from Ocarina of Time carved into the perimeter of the dome.
Yeah, there are a lot of different references. One that I think was very cool was the following:
Towards the end of the game, after Sky Keep, when Link had gathered all pieces of the Triforce, he and Fi are on top of the Goddess Statue and Link wishes for the destruction of Demise. When the Tricorce appears the three pieces float around very similarly to how they do it in the intro of ALttP.