You've seen my Inner and Outer Planes resource indices, well now here's on on the Far Realm.
WHAT IS THE FAR REALM?
The Far Realm, as described pre-4E, is a plane/dimension/reality independent of time, that exists outside the D&D Multiverse. It is inimical to both life and matter in the Multiverse, and its inspiration is based heavily on works from HP Lovecraft (mastermind behind the Cthulhu mythos) As of the end of 3.5, the Far Realm is only known to consist of the Amoebic Sea-- a multi-layered, (presumably) infinitely or practically infinitely deep ocean of green slime with empty air/space above, and planar pockets or even demiplanes of random terrain/elements/etc.
However, you can (and this is what I have done) decide that the Far Realm is an entire multiverse with its own cosmology, especially if you wish to encorporate creatures and dimensions from 3rd party materials.
It would be a myriad planes cosmology (see 3E Manual of the Planes), and under such provisions, at least 3 planes are known thus far to the cosmology. The most familiar is the Amoebic Sea, of course. The second one is a plane of cold and darkness from which Father Llymic and probably the Shivhads emerged, as suggested in Elder Evils. The third plane is that of the Luminas from the third-party Violet Dawn setting.
GENERAL RESOURCES:
Lords of Madness and Dragon Magazine 330 (Enter the Far Realm) are the essential sourcebooks/accessories you'll need.
You'll also want to pick up Elder Evils, as it gives some new additional info on the Elder Elves.
You might want to pick up the 2E adventure "The Gates of Firestorm Peak", which began the concept, though it is hardly necessary-- most of the story-related information can be found in Dragon 330, and the monsters have been updated elsewhere, so it's more of a curiosity than anything else.
You might also want to pick up the Eberron Campaign Setting book, as the Plane of Xoriat (which plays a major role in the campaign setting) is modeled/synonymous with the Far Realm (though you won't want to use the Xoriat encounter table as monsters in Eberron are often ascribed a different history/origin than what is found in Abeir Toril, Greyhawk, and Planescape settings) The Gatekeeper organization is also of interest, though it will have to be reflavored for Planescape, Abeir-Toril, and Greyhawk settings. Faiths of Eberron and the Eberron Campaign Setting are the best books for info on this organization.
FAR REALM POWERS AND QUASI-POWERS
This is a list of powers either native to and living in the Far-Realm multiverse, or living in the D&D multiverse, but not naturalized.
--Bolothamogg/Him Who Watches from Beyond the Stars (Lords of Madness)
--Father Llymic (Elder Evils) (currently imprisoned in a mountain on Oerth)
--Ghulurak (DMGII p. 115)
--Holashner/The Hunger Below (Lords of Madness)
--Mak Thuum Ngatha (Lords of Madness)
--Piscaethces/The Blood Queen (Lords of Madness)
--Shothotugg/Eater of Worlds (Lords of Madness)
--Thoon (Monster Manual 5)
--Y'chak/The Violet Flame (Lords of Madness)
--Zurguth/The Consuming Vast (Dragon 358)
FAR REALM NATURALIZED POWERS
The following are powers that exist in our multiverse but are partially naturalized.
--Ghaunadaur (Faiths & Pantheons, Demihuman Deities, Lords of Madness)
--The Great Mother (Lords of Madness)
--The Patient One (Book of Vile Darkness, Lords of Madness)
--Temulea (Violet Dawn campaign setting books)
--Tharizdun (Return to the Temple of Elemental Evil, Lords of Madness)
Here also is a vestige of a mortal woman who flirted with Far-Realm powers.
http://www.wizards.com/default.asp?x=dnd/frcc/20070718
FAR-REALM CONFIRMED ABERRATIONS
The following creatures are confirmed to be native to the Far-Realm or corrupted by it.
--Aleku (Dragon 348)
--Amoebic Crawler (Dragon 330)
--Bloodsipper (En World Converted Monsters)
--Brood Spawn template (Elder Evils) (associated with Father Llymic)
--Cloaker (MM)
--Cloaker Lord (Monsters of Faerun)
--Cloaker, Shadowcloak Elder (Lords of Madness)
--Cranial Encyster (Dragon 330)
--Daelkyr (Eberron Campaign Setting) (the appearance described in ECS should not be their true form)
--Dharculus (Planar Handbook)
--Dolgaunt (Eberron Campaign Setting) (created by Daelkyr)
--Dolgrim (Eberron Campaign Setting) (created by Daelkyr)
--Essence Reaver (Eberron: Secrets of Sarlona)
--Half-Farspawn (Lords of Madness)
--Gibberling Brood (En World Converted Monsters)
--Gibbering Mouther (Lords of Madness, Monster Manual 1)
--Kaorti (Fiend Folio, Dragon 358)
--Kaortic Hulk (Dragon 330)
--Kyra (Dragon 348)
--Mind Flayers of Thoon (Monster Manual 5)
--Neh-Thalggu (Epic Level Handbook)
--Nightseed (Dragon 330)
--Pseudo-Natural template (Epic Level handbook, Lords of Madness, Complete Arcane)
--Psurlon (Monster Manual 2, Lords of Madness)
--Scorrow (Eberron: Secrets of Xendrik)
--Snowcloak (Frostburn, Silver Marches) *member of the cloaker family*
--Squamous Spewer (Draconomicon)
--Tentacle Spider (Eberron: Secrets of Xendrik)
--The Thing From the Lake (Dungeon 134)
--Urquirsh (Dragon 358)
--Uvuudaum (Epic Level Handbook)
--Wyste (Monster Manual 2)
This is an Outsider, but it appears to be from the Far Realm (or would easily work as such).
Black Loper (http://www.wizards.com/default.asp?x=dnd/mm/20010831a)
I'm listing here the known origins of aberrations by category, as a resource for those who wish to create ones for those lacking such.
MAGICALLY CREATED
(This category includes any creatures of magical or psionic origin. I'm going to assume that other mimic monsters are also magically created since it's confirmed that the standard mimic is.)
Apodalypse (EN World Converted Monsters)
Athach (MM) (presumed but not actually stated)
Balhannoth (MMIV)
Bi-Nou/Rockworm (EN World Converted Monsters)
Bowlder (not sure if it was ever converted) *presumed all mimics are magically created, but not confirmed*
Braintree (EN World Converted Monsters)
Carrion Crawler (MM)
Catoblepas (MM2)
Choker (Dragon 323*)
Chuul (MM, Stormwrack)
Cursed Cold One/Gelun (Sandstorm)
Diamondback Viper (http://www.wizards.com/default.asp?x=dnd/mm/20001001a) *presumed but not confirmed; most likely creators were either humanoids or dragons.*
Dolghast (Magic of Eberron)
Dolgrue (Dragon 348)
Dragon, Brainstealer (Dragon 337)
Dustblight (Sandstorm) (presumably)
Dweomerborn (Spelljammer Beyond the Moons)
Elan (Expanded Psionics)
Firestar (En World Converted Monsters) *presumably created by the Windukes from air element/animental stock like the Hounds of Law*
Ghostlight (En World Converted Monsters) *presumably created by the Windukes from air element/animental stock like the Hounds of Law*
Hook Horror (MM2)
Howler Wasp (MM4)
Ineffable Horror (Underdark) (a safe guess, since it resembles mindflayers...)
Intellect Devourer (Expanded Psionics) (just a guess, since they're walking brains and domesticated by the Illithidae)
Julajimus (MM2)
Kython (Book of Vile Darkness)
Living Bridge (not sure if it was ever converted) (mimic-like creature confirmed to be magically created)
Lock Lurker (EN World Converted Monsters) *presumed all mimics are magically created, but not confirmed*
Lodestone Marauderer (MM4)
Lurking Strangler (MM3)
Mageripper Swarm (MM4)
Meenlock (MM2)
Mimic (MM)
Mimic, House Hunter (En World Converted Monsters) *presumed all mimics are magically created, but not confirmed*
Mind Worm (Dragon 337)
Naga (Monster Ecology, MM, Serpent Kingdoms)
Nasnas (En World Converted Monsters)
Nerve Swimmers (Dragon 337)
Nothic (Miniatures)
Nyth (Monsters of Faerun) *presumably created by the Windukes from air element/animental stock like the Hounds of Law*
Octopin (Dungeon 127
Opabiana (Dragon 348)
Palimpsest (never converted) *presumed all mimics are magically created, but not confirmed*
Peltast (EN World Converted Monsters) *presumed all mimics are magically created, but not confirmed*
Psi-Hulk (Expedition to Undermountain)
Ringworm (FR Monstrous Compendium II-- never updated) *presumed all mimics are magically created, but not confirmed*
Roper, Prismatic (MM3)
Rot Weaver (MM3)
Rukanyr (Fiend Folio) (created by the Kaorti)
Runehound (MM3)
Sharn (Anauroch, Monsters of Faerun)
Shrieking Terror (MM3)
Skum (MM)
Skybleeder (Fiend Folio) (created by the Kaorti)
Slasrath (Fiend Folio)
Spectral Lurker (Fiend Folio)
Spellwarped template (Monster Manual III)
Symbionts, Cerebral (Fiend Folio)
Thruock (http://www.wizards.com/default.asp?x=dnd/re/20031007a) *created by Kaorti*
Tooth Beast (Tome of Magic)
Umber Hulk (MM)
Vampiric Mist (EN World Converted Monsters)
Xantravar (EN World Converted Monsters) *seems likely, but not confirmed; possibly an aboleth creation*
Xaver (EN World Converted Monsters) *presumed all mimics are magically created, but not confirmed*
Xenostelid (Dragon 348)
Wharlysk (http://www.wizards.com/default.asp?x=dnd/fw/20030531a) *presumed but not confirmed*
Will-O-Wisp (MM) *presumably created by the Windukes from air element/animental stock like the Hounds of Law*
Witchlight (Spelljammer Beyond the Moons)
Zern Experiment, Arcanovore (MM4)
INDIGENOUS PLANAR/ INDIGENOUS ANTEDILUVIAN/PRECAMBRIAN
(As far as I can tell, these creatures are indigenous to some part of the multiverse.)
Abyssal Ant Swarm (Fiend Folio) *Abyss*
Darkweaver (Fiend Folio) *Shadow*
Ecto Fragment (http://www.wizards.com/default.asp?x=dnd/psb/20030725b) *Demiplane of Ectoplasm*
Ethereal Defiler (MM5) *Ethereal*
Ethergaunt (Fiend Folio) *Ethereal*
Fihyr (MM2) *Dreamscape/Nightmare Lands*
Flumph (Dungeon 118, EN World Converted) *Antediluvian; possibly created by the Aboleth*
Folugub (Expanded Psionics) *related to rust monsters; turns crystal to slime, likely also native to Thuldanin*
Nilshai/Ethereal Theurge (Unapproachable East) *Ethereal*
Odopi (MMIII) *Carceri*
Oozecrawler (Violet Dawn: Complete Book of Denizens)
Oozes (most) *prime, Inner or Outer planes*
Phiuhl (Fiend Folio) *Gehenna*
Roper (MM, Lords of Madness) *Antediluvian, probably a creation of the Aboleth*
Rust Monster (MM) *Indigenous to Thuldanin, a layer of Acheron*
Seryulin (MM3) *I'm just guessing here. Seems likely however if they're associated with Kuo-Toa. ...Why are these things aberrations rather than magical beasts, anyway?*
Shadow Creature template (Lords of Madness) *Shadow*
Spirrax (MMV) *native to a dying demiplane*
Synad (Complete Psionic) *parralel world accessible through the Plane of Shadow*
Yurian (Fiend Folio) *Antediluvian?*
OUT OF TIME *Future*
Carrion Crawler (MM) *from the end of time/the Multiverse like the Illithidae*
Illithidae (various)
Sithilar (Lords of Madness)
POWER-CREATED
(This list includes any creature created or altered through the direct intercession of a deity.)
Aboleth (MM and Lords of Madness) (Piscaethces/The Blood Queen)
Aracholoth (Dragon 298) (Lolth)
Beholders (MM and various) (Great Mother)
Brood Mother (Dragon 298) (Lolth)
Choldrith (Monsters of Faerun) (Lolth)
Chwedenja (FF, Drow of Underdark) (Lolth)
Destrachan (MM) (might be created by a Far Realm power)
Drider (MM) (Lolth)
Ettercap (MM)
Fachan (EN World Converted Monsters) (Gruumsh)
Gibbering Orb (Epic) (Great Mother)
Naga, Worm (Dungeon 130) (Kyuss)
Shunned (Drow of the Underdark) (Lolth)
Spiderleg Horror (Dragon 298) (Lolth)
OUTER SPACE
(Creatures native to a planet other than the main prime ones-- such as Aebryinis, Athas, Eberron, Krynn, Mystra, Oerth, and Toril)
Bonetree (Dragon 280) *not an aberration*
Chilblain (Frostburn) *not explicitly stated, but it does say they're native to the Material Plane.*
Contemplator (Spelljammer Beyond the Moons)
Fal/Falmadrattha (Spelljammer Beyond the Moons)
Focoid (Spelljammer Beyond the Moons)
Gravislayer (Spelljammer Beyond the Moons)
Lutum (Spelljammer Beyond the Moons)
Meteorspawn (Spelljammer Beyond the Moons)
Moonbeast (MM2)
Moonlord (Dragon 340)
Murderoid (Spelljammer Beyond the Moons)
Neogi (MMII, Lords of Madness)
Ragewing (Dragon Compendium, Dragon 280)
Razortail (Dragon 280) *not an aberration*
Stonesinger (MM3) *not explicitly stated, but it does say they're native to the Material Plane.*
Treeleg Strangler (Dragon 280)
Trelon (EN World Convered Monsters)
Tsochar (Lords of Madness)
Umber Hulk (MM) *might be magically created; associated with Neogi*
ALTERNATE MATERIAL PLANE
Grell (MM2, Lords of Madness)
Nishruu (not sure this was ever converted)
UNKNOWN
Though I have yet to exhaust 2E resources for some of these monsters (to see if their origins are mentioned there), I have yet to find anything in 3x resources which determines their origin.
Adherer (EN World Converted Monsters)
Ahuizotl (Fiend Folio)
Annihilator (Underdark) *very similar to rust monster, but disintegrates living creatures instead*
Avolakia (MMII) *possibly a creation of the aboleth*
Boneleaf (Heroes of Horror)
Corruption Eater (Heroes of Horror)
Crystalmist (EN World Converted Monsters)
Darktentacles (MMII)
Deadly Dancer (Tome of Magic)
Deepspawn (Lost Empires of Faerun)
Delver (MM)
Denzelian (EN World Converted Monsters)
Ephemeral Hangman (Tome of Magic)
Faze (http://www.wizards.com/default.asp?x=dnd/ae/20030826a) *found on Astral, but uncertain if indigenous*
Foulwing (Lost Empires of Faerun, City of the Spider Queen WE)
Garbler (Tome of Magic)
Glasspane Horror (Dragon Magazine Compendium)
Grick (MM)
Gutpuppet (http://www.wizards.com/dnd/article.asp?x=dnd/mm/mm20011215a)
Hagunemnon (Epic)
Horgar (EN World Converted Monsters)
Hound of the Gloom (Lords of Madness)
Ixitxachitl (MMII)
Krakentua (EN World Converted Monsters)
Lurker (Underdark, City of the Spiderqueen WE) *possibly the Far-Realm like the Cloakers*
Lythlyx (EN World Converted Monsters) *possibly a creation of the Aboleth, or a larval stage of certain psionics-using tentacled creatures*
Mad Slasher (Miniatures)
Malasynep (Frostburn)
Maulgoth (Fiend Folio)
Mindshredder (MMIII)
Mindstealer (http://www.wizards.com/default.asp?x=dnd/mm/20030727a)
Ocularon (Fiend Folio)
Orpsu (EN World Converted Monsters)
Otyugh (MM) *conceivably a creation of the Aboleth*
Phaerimm (Lost Empires of Faerun, Monsters of Faerun)
Phasm (MM)
Quaraphon (MMIII)
Ripper (Cityscape)
Shadow Choker (Lords of Madness)
Shivhad (Frostburn)
Spark Lasher (Miniatures)
Harpoon Spider (MMIII)
Steel Shadow (EN World Converted Monsters)
Susurrus (MMIII) *not the same as the 2E sussurus*
Tall Mouther (Shining South, Monsters of Faerun)
Tentamort (EN World Converted Monsters)
Thorciasid (Epic)
Tinkerer (Spelljammer Beyond the Moons)
Tunnel Terror (FF) *distantly related to delvers*
Vermiurge (Epic)
Vivisector (MMV)
Windghost (MMII)
Zeugalak (LoM)
I'm leaning towards magical creation for the malasynep and treat the Shivhad as Far-Realm indigenous (presumably from the same dark, cold plane as Father Llymic). Seems like there should be an optional-rule psionic variant of the malasynep; I'll get to making one eventually.