3? Only 3? But, but,... alright.
Defining "core" as anything in the SRD, and keeping it focused on 3e:
Book of Hallowed Might, Malhavoc
Legions of Hell/Armies of the Abyss, Green Ronin
All of the various Counter Collections, Fiery Dragon
These are just about the only supplements I have that I'm using *everything* from.
Manual of the Planes, WotC
Oathbound, Bastion
Traps & Treacheries
Three very strong runner-ups. MotP is perhaps the best GM's supplement from 3e, even if I did throw out most of its material because it dealt with the standard 3e cosmology. Oathbound's probably going to have some of it's prestige classes and races dropped, but it's mostly just a snap-in. As for T&T, I dropped 1 or 2 of the PrCs, but it's full of all kinds of PC-killing goodness.
d20, not 3e related:
Traveller d20