Crystal Skulls (all of them supposedly located, 30/30 pictured [1 pic on accident])
Chapter 01
~ 01 - From where you obtain the Art of the Inferno, go towards the room's exit and jump to where the first Skull is.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-01.png
~ 02 - Nearby the archer perched on a walkway, Bird Flip off the nearby tree to land on an adjacent walkway.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-02.png
Chapter 02
~ 01 - Under the main bridge, you can't miss it.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch02-01.png
~ 02 - When you do the platforming to get the jewels to proceed furthur in the castle, this skull is a little bit away from the Vermilion jewel. Break down the walls, go past the dead body, watch out for the trap door and there it is. Or you could just go from the Ultramarine Jewel, break down the wall and there it is. Either path is fine.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch02-02.png
Chapter 03
~ 01 - Top of the first fire escape you go up in.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch03-01.png
~ 02 - When you go underground, you will eventually drop down to a small room with enemies and a Ninja corpse with arrows in it. After leaving it, head left and you'll find the Ninja with the "Invisible Path" tutorial. Do some wall running to reach the skull.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch03-02.png
Chapter 04
~ 01 - After exiting the subway, go past the rubble on your right and go into an alleyway which is again to the right. This alleyway does a loop and exits onto the same street. Do some wall running to reach the fire escape with the skull.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch04-01.png
~ 02 - You can't miss this. Its right next to a ladder you jump to from a bridge to proceed.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch04-02.png
~ 03 - In the Statue of Liberty on a steel girder from a save point. Don't remember exactly where, but pay attention to a bunch of girders in a room.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch04-03.png
Chapter 05
~ 01 - On a boat at the first area, across from the Kusari-gama the dead ninja has.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch05-01.png
~ 02 - On a table to your right after passing by the door with the Earth Dragon Statue.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch05-02.png
~ 03 - After getting the Gatling Spear Gun (GOMU GOMU NO....), swim a bit, pay attention to a branch to your right, shoot a bunch of mines, and try to get to the corner with the skull.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch05-03.png
Chapter 06
~ 01 - Across from the first Muramasa statue.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch06-01.png
~ 02 - When you exit out of the body dump area using the Bird Flip, immediately next to you is a guillotine. Slash the rope on the side to make the blade drop and the cover at the bottom move out of the way to reveal a Crystal Skull.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch06-02.png
~ 03 - After getting and using the Cast Iron Key, you'll reach an Earth Dragon Statue and the next room you'll find a bunch of books. Slash the bookshelves on the left to reveal this Crystal Skull.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch06-03.png
Chapter 07
~ 01 - Left of the Control Room's controls.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch07-01.png
~ 02 - After you get the Tonfa (I think) you'll wind up back in the first room where you hear the guy on the intercom for the first time. It'll be in some debris to your right.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch07-02.png
Chapter 08
~ 01 - In some snow under the windows where all the RPG guys were shooting at you from a distance
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch08-01.png
~ 02 - After using the Bell Key, it'll be in an alcove with candles while you're descending the stairs.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch08-02.png
~ 03 - In the train on a table.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch08-02.png
~ 04 - On a spinning cog. Can't miss it I guess. Just don't get crushed.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch08-04.png
Chapter 09
~ 01 - When you reach the area with the spotlights, run across to the far right dock. The skull is on a rope with other normal skulls. Its easy to see since its night.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch09-01.png
~ 02 - When you start monkeying your way across a rope to reach the other side, stop about 3/4 and look to the right to see a skull. Swing from rope to branch until you reach the skull
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch09-02.png
~ 03 - After you exit the tunnel and wind up in an area with an enemy encounter, this skull is to the right next to some rubble.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch09-03.png
~ 04 - After the cutscene with the BSN dead in the river, jump in and turn around to find it.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch09-04.png
Chapter 10
~ 01 - When you get to a part where you have to run from wall to wall, you should see it above your head. Just do the wall runs, turn around, then wall run to it.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch10-01.png
~ 02 - When you go down a big descending stairs, keep looking to your left, you should see it in the distance behind a small wall.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch10-02.png
Chapter 11
~ 01 - Okay, I didn't pick this up, but I saw a faint glow of it in my video. In the Hayabusa village, go down the alleyway right next to the main entrance (the waterfall one), you'll find a dead body (just like the last game!), go down into a tight corner and you'll find the skull under a wheel. If you look at these pics, you'll notice a faint glow in the 2nd/3rd ones. God DAMMIT!
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch11-01-MissedButFound01.png
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch11-01-MissedButFound02.png
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch11-01-MissedButFound03.png
~ 02 - After emerging from the water tunnel and fighting enemies in a weedy area. Break the door off the small shrine.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch11-02.png
~ 03 - When you wind up back at the Ninja Fortress' entrance, jump down to where you start out in the last game (no dead body here?), then go to where you get the Fire Wheels last time, there is a skull in place of it.
http://i48.photobucket.com/albums/f219/Jinjo402/Ninja Gaiden II/CS-Ch11-03.png
And that's it.