Bloody Tears is used in:
-CV2 (original)
-Haunted Castle (very close to original)
-Bloodlines (essentially original, but instrumentation weakens it)
-Super CV4 (intro is changed, some chords are different)
-X68000-Rondo/DXX (Rock version, added a guitar riff)
-Rondo/DXX (added a n organ requiem at the end, thus establishing it as a chapel tune)
-Nocturne in the Moonlight (absolutely different!)
-Legends (Super PowerRock, very different chords)
-Dawn of Sorrow (with some slight chord changes, it's mostly the same as Rondo of Blood)
-CV64/LoD (just an organ riff, though in the crypt in the villa it uses very eerie chords)
-Judgment. (Very nice rock version)
...did I forget any?
Theme of Simon has been used in:
-Super CV4 (original, has four-note intro)
-X68000 (this version has the fanfare as its intro, plus brasses in the 2nd section)
-Bloodlines (similar to X68000, some slight chord changes)
-LoD (just a small fanfare when Henry rescues the children)
-Circle of the Moon (unused but in the game data, just a fanfare)
-Portrait of Ruin (similar to the MIDI power pro disc version)
...did I forget any others?
For both themes, I did not mention other disc versions.
EDIT: Fixed a little reverse I did, there.