Some choices in the game (i.e. Triss vs. Shani) really have little to do with Geralt's factional neutrality, although they are no less interesting with respect to plot and some rather important story consequences.
However, for the factional conflicts:
In "Force Recon", one remains neutral by refusing to lead the Order assault against the elves. However, I received no negative consequences for completing this mission and was still able to be neutral later. During "Gold Rush", you have to choose sides to eliminate the possibility of helping one side in the "Free Elves" quest. If you help, say, the elves, in "Gold Rush" you have the option of helping the elves or remaining neutral in "Free Elves". Same thing if you choose to help the Order in "Gold Rush": you can help the Order or remain neutral in "Free Elves".
Inevitably, only "Free Elves" is the mission where you decide to be neutral or not, although if you are planning to side with the Order or with Yaevin, you have to choose their sides during "Gold Rush".
Post edited July 09, 2011 by scollins1987