It's a tie:
1. Delta Green: I love Delta Green. It's great. I've never actually seen a live copy of Countdown, so I have difficulty believing it might be better.
2. Universal Brotherhood: I don't care as much for the module part, but the fiction part runs a chill down my spine whenever I read it.
3. The Tyranny book for the original version of Rapture: The Second Coming.
Now, none of these books have been all that useful to me. My group just doesn't groove on CoC overall, and when they have been open to it, it's been the 20s, not the Nows.
The group loves SR, but I just can't make the spirits as creepy and evil as presented in the UB.
Nobody in my group even wants to bother trying to play Rapture.
But useful or not, those are my favorites.