Lowest CR Gargantuan giant or humanoid before acquired templates?

[Elves]

Best I can find are

half-troll ibrandlin (Monsters of Faerun) -- CR 5
variant half-fiend (Huge parent) phaerlin giant/OA constrictor naga -- CR 6

[ShurikVch]

Gargantua (http://www.pandius.com/gargntua.html) Giant Firefly (Arms and Equipment Guide) Half-Troll CR: ½*4+2=4
Gargantua (http://www.pandius.com/gargntua.html) Giant Strider (Monsters of Faerûn) Half-Troll Proto-Creature CR:1*4+2-2=4
Gargantua (http://www.pandius.com/gargntua.html) Ur'Epona (Planar Handbook) Half-Troll Proto-Creature CR: 1*4+2-2=4

Mountain Creature (Faces of the Forgotten North) Unseelie Fey Huge Monstrous Centipede Half-Troll Proto-Creature CR: 2+3+0+2-2=5
Mountain Creature (Faces of the Forgotten North) Hypnosnake (Dangerous Denizens) Half-Troll Proto-Creature CR: 2+3+2-2=5

Also, note - Half-Fiend variant rules may not increase size in that case:

A very small number of fiends are Huge, and their hugeness gets passed to offspring. If the model fiend is Huge size or bigger, and the base creature is size Large or smaller, then increase the base creature's size by one category. The relevant changes to the base creature's statistics can be found on page 291 of the Monster Manual. If the base creature increases in size, increase the CR of the final creature by 1.
Thus - doesn't works for sizes above Large

EDIT:
The lowest CR possible would be 2:
1) Rock Troll (Dragon #286) - 4 HD Large Giant; CR 1
2) Gargantua (http://www.pandius.com/gargntua.html) template - +2 size, HD*4=16; CR*4=4
3) Dark Creature (Cormyr: The Tearing of the Weave), Quasilycanthrope (https://web.archive.org/web/20130531114642/http://www.wizards.com/default.asp?x=dnd/mb/20040721a), or any other +1 CR inherent template which grants spell-like or supernatural SA, and don't change the type; CR 4+1=5
4) Proto-Creature template (Bestiary Of Krynn, Revised) - -3 CR for creatures with more than 13 HD who has spell-like or supernatural SA; CR 5-3=2

[Elves]

Interesting stuff Shurik. The Mystara content is homebrew though, it's a designated fansite not officially licensed. You're right the half demon doesn't work which leaves us with the ibrandlin.

Proto creature definitely interesting to reduce CR although LA +0 makes it completely borked for PCs; I assume the writers didn't understand the game and meant LA --.

To take advantage of proto creature you could do an incarnate effigy titanic animal which gets you base CR 7 with 25 HD, -3 from proto = 4.

[ShurikVch]

You're right the half demon doesn't work which leaves us with the ibrandlin.
Note: Half-Troll Ibrandlin would be CR 7 - not 5 (Half-Troll is CR +2)


Proto creature definitely interesting to reduce CR although LA +0 makes it completely borked for PCs; I assume the writers didn't understand the game and meant LA --.
You're missing important moments there:
a) Proto-Creature's body disintegrates on death, which makes it impossible to raise them
b) Hit to mental stats makes it undesirable for casters and skillmonkeys (except for those which are Wis-SAD)
c) Removal of SLA and SU limits with which classes it can realistically work with


To take advantage of proto creature you could do an incarnate effigy titanic animal which gets you base CR 7 with 25 HD, -3 from proto = 4.
1. The thread's name says "before acquired templates"; Incarnate Construct is acquired template
2. Incarnate Construct removes all SA and SQ; for creatures without any SLA or SU, Proto-Creature is flat +1 CR