Recenetly I have been trying to track down all of my favorite childhood movies. When I was younger I remember watching an animated movie about a little boy. The only thing I remember is at the very end he is in a castle and it is destroyed by a sludge like substance. I thought the title was Secret of Nimh but that is something different. I know the title has to be along those lines. It's animated so I don't know the actors and I don't even know the title so I have o idea how to find it.

Do you know when you saw this film? The only animated movie with Nimh in the name that I can remember is Rats of Nimh, but as you've said, it's not that one. Also, do you recall any magic or swords being used? There are just so many film possibilities, like The Black Cauldron and such. Just need a little more info.

Possibly "Little Nemo: Adventures in Slumberland" (1989) It's about a little boy named Nemo who has a problem keeping his promises. In his sleep he travels to slumberland and is befriended by King Morpheus. The Princess fancies Nemo and makes him her playmate. King Morpheus gives Nemo a key that can open any door and makes him promise not to open the door with the same symbol as is on the key. Nemo promises but influenced by Flip (voiced by Mickey Rooney) The no-good clown, he opens the forbidden door and unleashes the Nightmare (which is the part with the castle and the goo) When the nightmare is unleashed a black goo fills the palace during Nemo's coronation as Prince of Slumberland and kidnaps the king. As Nemo was the only one in possession of the key he is blamed for the loss of the king and embarks on a journey to Nightmareland with the princess the kings adviser and Flip who has the one and only map of Nightmareland. Together they rescue King Morpheus and destroy the nightmare king forever.

Hope that helped! If not sorry :(

Edit: I know the name isn't the same, but Nemo starts with an N same as NIMH and Slumberland starts with an S same as Secret so it may be your answer :)
And The Secret of NIMH has a scene where Mrs. Brisby's house (a cinderblock) is sinking into a mud puddle and filling with mud while her children are still inside so you were on the right track.