What are the brain structures directly on top of the brain stem?
You're looking at many structures in this area. 

The region directly above the midbrain is the diencephalon (meaning "across + brain"). From inferior to superior it's composed of the hypothalamus, thalamus, and structures that developed from a developmental region referred to as the epithalamus that include the pineal gland, habenular trigone, and choroid plexus. Between the hemispheres of the thalamus/hypothalmus lies the third ventricle (which may be "bridged" by a structure called the interthalamic adhesion). 

Of each of these structures, only the thalamus and hypothalamus are truly visible from your images -- with the hypothalamus articulating with the midbrain and the thalamus emerging superior and slightly lateral to he hypothalamus. The following structures are also visible in your image:

The most inferior structure you see is the pituitary gland, while the "X" shaped structure superior to it is the optic chiasm with cut optic nerves anteriorly and optic tracts continuing posteriorly out of view. 
It's not entirely clear, but I believe the two protruding structures posterior to the pituitary are the paired oculomotor nerves. 
Finally, the two long ribbon-like structures that extend anteriorly are the olfactory tracts of cranial nerve I that terminate anteriorly in optic bulbs.