I'm really quite fond of some of the solo albums that came out around the comic's heyday, particularly Mobius Trip and Hadron Kaleido, Medium, Sburb, and One Year Older. All of them are such wonderful albums, each full of spectacular music.
Though I suppose that my favorite song is probably Ruins (With Strings) by Erik Scheele and Michael Guy Bowman from Homestuck Vol.5. I just love the feeling the song gives off with its soundscape. The heavily reverberated piano is accompanied by the sound effect of the blowing wind, the way the guitar plays the main melody over top the piano when the strings are introduced. The way that the song gives off a desolate and lonely sound in the beginning, then swells into a melancholic small symphony in its later half. I just find it absolutely amazing.