[ninlaith]

I loved all the extra footage in ROTK

When Eowyn sang the lament for Theodrid, shades of Tolkien's favourite book Beowulf.

When Eowyn shared the cup with Aragorn, also shades of Beowulf.

The name Meduseld, also shades of Beowulf. Meduseld was where Hrothgar resided in Beowulf.

Legolas and Gimli's final count on orcs

When Merry and Pippin are at Isengard with Treebeard and they're looking at Isengard saying "It's a quality establishment." and so forth sounding like a hotel brochure.

When Pippin and Merry are looking for food at Isengard and Pippin finds an apple and looks up like it came from the sky just like when Aragorn hit him with the apple.

You guessed it...When Aragorn hit Pippin with the apple in FOTR

In Moria when the fellowship is waiting for Gandalf to decide which way to go. If you listen very very closely you hear a conversation between Merry and Pippin...
Pippin:.....Merry!
Merry:....What!
Pippin:..........I'm hungry!