Dr. Fate's helm on the shelf next to Haro. Animated vessel of the all-spark in the bottom right. Key to Vector Sigma next to the millennium puzzle, or possibly Sari's key from animated.

Mastine said:

Dr. Fate's helm on the shelf next to Haro. Animated vessel of the all-spark in the bottom right. Key to Vector Sigma next to the millennium puzzle, or possibly Sari's key from animated.

Added annotations for these and the other ponies. Only things left now are the starship thing next to the Matrix of Leadership, the thing that looks like an egg near Bumblebee, the mushroom guy, the claw, and the green thing in the container behind the energon cubes.

frenzy is the blue one and rumble the red one

The ship next to the Matrix is the Lost Light from the IDW comics.