Apparently in the original version you fought the Skull Knight in a very different room. The beta is on top, the final is on the bottom. The change isn't anything big but still worth mentioning.   New stuff is at the bottom (until I eventually redesign the page..)

The Wind spellbook and Bible combination looks a lot like the shields from Gradius 3.

In the background of the Skeleton Cave in Castle B are two skeletons.  Both happen to look a lot like Slogra and Gaibon.

The Battle Arena from Harmony of Dissonance in Boss Rush mode (top) is obviously modeled after Symphony of the Night Coliseum room.  Konami did a good job of doing it.  Thanks to Jorge D. Fuentes for the SotN Battle Arena image.

A statue of Dracula's third form from Castlevania III: Dracula's Curse is in the Skeleton Cave of Castle A.

Also in the Skeleton Cave of Castle A is a skeleton of Medusa.

And in just the opposite place in Castle B is the same skull as on the sides of the SotN warps.  Also you could go as far as to say it's of the big three eyed ghost from Rondo of Blood (image coming soon).