I'll have to second the nomination of
Dark*Matter; it was the first thing that leapt to mind when I read the OP. Love it.
I would also mention
Best of The Dragon, vol 1. I can't think of any other supplemental product I re-read as often when I was a wee gamer.
As for
Runequest... anything from the RQ2 era is excellent. As much as I loved paging through my Cthulhu/Nehwon/Melnibone-inclusive
Deities & Demigods back in the day, you put it next to
Cults of Prax and... there's just no contest.
Looking at some of my more current books, Goodman Games'
Power Gamer guides probably get the nod in the d20 category. Of the piles of d20 supplements I've owned, they've been the most useful and most fun to read.
Looking beyond d20... it's the
Monster Burner for
Burning Wheel. Best monster book ever for the best FRPG since... well, RQ2.
