This is what I've found so far:
CR +0 templates
Bone Creature (BV)
Dragonborn of Bahamut (RDr)
Dungeonbred Monster (Du)
Necropolitan (LM)
Primordial Giant (SX)
Tainted Raver (HoH)
Yuan-ti Broodguard (SS)
Dark Creature (TM) (CR +0 or CR +1 depending on the base creature)
Vecna-blooded (MM5) (after the template has been lost, only the Cloak of Mystery ability remains)
Xorvintaal Dragon (MM5) (rises to CR 1+ if extra abilities are added)
CR +0 when applied to creatures of 3HD or less
Anarchic Creature (PlH)
Axiomatic Creature (PlH)
Celestial (MM)
Element Creature (MP)
Entropic Creature (PlH)
Fiendish (MM)
Psuedonatural (LoM)
Spellwarped (MM3)
CR = 1/2
Incarnate Construct
DMG2 CR+0 NPC traits
Graced from outside
Guardian spirit
Lifemate
Poisonlaced
Prodigy