Speaking for myself, my active thought process is involved in simultaneously hearing all the components in the ensemble, including their trajectory up to that point, keeping both a physical (musical) and emotional (to me) analysis going in real time, and then concentrating very hard to contribute a part that relates to the other musical elements in a way that expresses my sense of where the piece may go (giving weight to certain pitches or intervals, density, speed, stasis), that is emotionally true from my understanding.
There are many axis where musical elements may resolve any number of ways, and it is the interplay of the ensemble, their musical analysis and emotive gambits, that determine the course of the performance. There's something about it simultaneously being a performance and a musical "composition" that weighs my choices toward my emotional responses.
It's this process being a central component of the performance that hasn't been articulated too clearly, and what sets it apart from the performance of a composition. Musically, there's so much that's similar - both have plenty of structural relations and emotion behind it. The great appeal improv has for its audience is that the creation unfolds before them in real time (never before, perhaps unique), taking the emotional temperature of the here and now. My goal as an improviser is to make musical connections - not as many as I possibly can, but the ones that draw a mood or emotional association or some picture in the mind, and build a cohabitive structure that has some musical integrity. My thought components, primarily musical information, are those that will contribute to this structuring. It's more difficult to trace the emotional side's contribution towards a successful performance. I can only point to the pre-human origins of music, and say we're wired for it - especially the here and now part
The performance itself, however, seems more of the point. The aleatory element inhibits a specific naming of a musical component being behind the thought process, though many are used quite consciously. There's a point where surrender to a group conjuring takes place, antithetical to a single composer's control of all the parameters.