I wondered about this too. My research advisor said it wasn't important, and told me not to bother reporting the results unless I got a very high score. I took it before I was told it didn't matter, and got 76th percentile since I hadn't yet finished my theory coursework and since my curriculum was sorely lacking in systems courses (I had one at a pretty basic level, basically nothing about operating systems or networking at all).
I didn't report my subject score to most of the places I applied. However, for some reason when I was looking at FAQs etc. I became convinced that Princeton were especially insistent that applicants submit a subject score, so I went ahead and sent it to them.
So if I get accepted everywhere but Princeton or rejected everywhere but Princeton (both highly unlikely, or at least the former is definitely unlikely and the latter is hopefully unlikely), maybe we'll have a better idea about the difference it makes