I finished Sandship last night, and I LOVED it. The boss was also a great one, and I enjoyed the journey over to the Sandship too. I'm enjoying Skyward Sword so much!
The Great Deku Tree truly sticks out in my mind as one of the best experiences I've had while gaming for many of the reasons you listed. There's just so much nostalgia attached to OoT in general for me, but especially that first dungeon. I can remember my friends at school imitating the tree...
Favorites (in no particular order): Arbiter's Grounds (TP), Lakebed Temple (TP), Snowpeak Ruins (TP), Great Deku Tree (OoT), Spirit Temple (OoT), Forest Temple (OoT), Stone Tower Temple (MM)
Least Favorite: Water Temple (OoT).