1- What writings of the Vilna Gaon do we have that are not commentary or textual emendations?
2- Do we possess any writings of the Vilna Gaon that talk about or reference his contemporaries or students?
There are around two dozen works from the Vilna Gaon that are still in manuscripts or destroyed (a work on astronomy, for example). From what has been published, the writings that are not commentary or textual emendations include:
You will find references to contemporaries in his letters. The most famous are his letters to rabbis in Lithuania and Belorussia instructing them to repudiate Hasidic leaders and their teachings. In addition, there are letters that he sent to his family (Iggeret HaGra) and close associates, such as the letter to his best friend, the Dubno Maggid, urging him to come and visit.
Even Shleima: an ethical treatise as well as kabbalistic ideas
Iggeres HaGr"a: this was a letter that the Gaon penned to his family before he left for his journey to Israel (which he ultimatly did not complete)