"The Secret Whispers" and "The Silent Forest". Recognize the names and themes? You should, because these two tracks play for Dwarf Woodlands and Enchanted Dominion respectively. Mixing the original themes together with "Night of the Dark Dream" certainly gives the feeling of their worlds being subsumed into the Realm of Darkness. If only the Castle of Dreams had its own Realm of Darkness version of "Bibbidi-Bobbidi-Boo"...
Aqua's theme gets a nightmarish Dark Reprise consisting of piano arranged much like a Scare Chord with sad violins thrown in for good measure. It is used as the boss theme for Phantom Aqua, who embodies all of Aqua's doubts and represents the Realm of Darkness' attempts to break her.
The final boss theme for 0.2 Birth by Sleep -A fragmentary passage-. "Wave of Darkness" had actually become so popular a song that Square-Enix ended up using it as essentially the "unofficial" theme of Kingdom Hearts III, often using the Orchestral version as the main background music of each of its trailers since 2.8's official release.
Kingdom Hearts Melody of Memory
"Dearly Beloved" gets a gorgeous jazzy cover that perfectly embodies the celebration of Kingdom Hearts's music that is Melody of Memory - and though the game doesn't introduce many new tracks of its own, the mere fact that Kingdom Hearts got a whole game devoted to its music just shows how incredible it is.
The theme associated with Roxas, "The Other Promise", also gained its own orchestral version. Most of the song is spent building up, but the final climax brings both chills to the spine and a tear to the eye.
There's also "Twinkle Twinkle Holidays", an orchestration of the theme used in Christmas Town. While not epic in the same way as the others listed here, it is still worth mentioning.
What takes the cake, though, is the masterpiece known as "The 13th Anthology". Yoko Shimomura took every single track within the games that had used Another Side's central theme (and The Encounter), and worked them together into one goosebump-inducing song.
Yoko Shimomura's second compilation album, Memória!, has a new arrangement of "Vector to the Heavens", Xion's theme. The 1:30 preview needs to be heard. The full version is the work of angels, no pun intended.
The "Concert Paraphrase on Dearly Beloved", which is probably the greatest "Dearly Beloved" piano arrangement that exists. This version's epicness comes from the feeling of climbing stairs as you listen to it. With the simple, standard Dearly Beloved at the beginning of the album, this awesome piece bookends the album with a virtuoso presentation of a fairly simple melody.