Hmmm...
EHRGEIZ Original Soundtrack - They left out the victory jingles used for the FINAL FANTASY characters.
Crisis Core: Final Fantasy VII Original Soundtrack - Missing the Victory Fanfare tune and a slight variation of
"The Summoned".
Tenchu SOUNDTRACK - "Battle with the Foreign Pirate",
"Battle with Onikage",
"Battle with Lord Mei-oh", instrumental version of
"add'ua (Opening Theme)" [serving as BGM for the Training level].
Tenchu 2 Soundtrack - The short piece of music heard at the main menu.
Shinobi Original Soundtrack - "Result Screen" tune.
Devil May Cry 2 Original Soundtrack - "Nightmare - Hwal Band". It was used to promote Devil May Cry 2, if memory serves me right.
Kessen II Original Soundtrack - "Ide Mariko - Ao No Tsuzuki" [Ending song].
Soul Reaver Promotional Soundtrack - "Ozar Midrashim" (I know it's included on the Information Society 'Don't Be Afraid' album, but it would have been nice to have it here, too).... And basically the whole soundtrack, spectral realm variations included ç_ç
These are the ones that come to my mind right now.