Ohhh boy. Well, the Silent Hill games have already been mentioned, so I'm gonna put my vote in for the Shadow Hearts series. Truly some of the most cracked-out monster designs I have ever seen. A few examples:
-a German Shepherd with a human arm where its face should be; it balances on the hand and attacks by hopping up to you and beating you with the dog
-a giant frog with human faces for eyes and a bloody hand for a tongue
-a human infant with a huge ball of random body parts where its legs should be
-the Rage Demons. Just...the Rage Demons. Yeah, that's supposed to be an umbilical cord sticking out of the front of them, but I DON'T BELIEVE IT. XD
I would also like to nominate the Xeobs from Lands of Lore: The Throne of Chaos. Garishly-colored Lovecraftian things with shapeless bodies, vertical mouths, tentacles, and the ability to spit acid. Gyargh.