Any faction would find clerics useful -- even the Athar have priests of the Great Unknown -- but clerics of particular gods or belief systems will either be namers only, or divided in their beliefs, unless they honestly consider their religion and their faction philosophy to meld into a single spiritual path. More common than such theological balancing acts might simply be those clerics who draw their power from the faction philosophy.
Clerics zealously devoted to a philosophy can draw strength from it as followers of a deity can draw from their gods, and "zealous devotee of a philosophy" is pretty much the basic description of a wide-ranging cross section of Sigil's population.
Though these clerics would have their individual interpretations, most likely certain spells would be very common, and enterprising research theologians might well isolate from the faction's belief domains specific to those tenets. Such an achievement would certainly mark a philosophy as worthy of note, capable of organizing a cleric's spirituality and granting power in return for adherence.
This is a suggested spell list for Domains that arise from fervent faith in a faction's philosophy, and some possible granted powers. These Domains would also be useful for arcane casters taking the Arcane Disciple feat from Complete Divine; for the Knowledge (religion) requirement of that feat substitute Knowledge (factions and guilds) if the game is using this skill from the PSCS.
The spells listed come from the 3.5 SRD, and sometimes the PSCS. In a Pathfinder game, remove the granted powers and select from among the spells listed those of roughly appropriate level to give clerics at the appropriate experience thresholds as "you can cast 1/day" abilities.
The granted powers may occasionally be useful as 1st-level domain abilities; higher level faction feats that usually require prerequisites could substitute for later levels.
The granted powers probably would frequently be either "+1 caster level on domain spells," or faction feats from the PSCS, generally the ones with no other significant prerequisites. Unique granted powers are certainly possible, though. A few suggestions are given, along with other standard Domains that zealous belief in a faction philosophy might provide as a cleric's second Domain choice.
Granted Power: Once per day, you may pit your belief against that of
a cleric of a specific deity. Make opposed caster level checks using
your caster level in the class that grants you the Athar Domain. If you
succeed, your words echo in his heart, distracting him: for 24 hours
any divine spell that cleric casts requires a Concentration check at a
DC of 10 + your caster level.
Other possibilities: Faithless Blessing.
1st: Remove Fear
2nd: Gentle Repose
3rd: Remove Curse
5th: Spell Resistance
8th: Spell Immunity, Greater
9th: Mage's Disjunction
A cleric devoted to the Great Unknown often manifests the Knowledge Domain. Any faction priest could probably select an appropriate alignment Domain.
Believers of the Source Domain, Godsmen Domain
Granted Power: possibly Cumulative Life Experience, or Talents of the Past.
1st: Endure Elements
2nd: Restoration, Lesser
4th: Polymorph *
6th: Legend Lore
8th: Planar Ally, Greater
* The forms available through this Domain spell are limited, and
vary from Godsman to Godsman; they believe the spell gives them access
to the forms of past lives. It always grants the same form to any
particular being, though these will differ among beings. It is
theoretically possible, one supposes, for an intelligent being to be on her first
life -- in which case this spell would not function! The Believers of
the Source would be extremely interested in such a person.
Priests of the Source frequently manifest the Creation Domain.
Bleak Cabal Domain, Bleaker Domain
Granted Power: Already Mad, Apathy, or the granted power of the
Madness Domain from Complete Divine. Numb (a PSCS Dustmen feat) would
2nd: Calm Emotions
3rd: Deep Slumber
4th: Crushing Despair
5th: Barmy Touch (PSCS)
6th: Symbol of Fear
8th: Symbol of Insanity
Bleaker Priests might manifest the Domain of Madness as well.
Granted Power: Destruction Embraced, or Sift.
1st: Entropic Shield
4th: Weight of Entropy (PSCS)
5th: Ecstatic Decay (PSCS)
8th: Horrid Wilting
Appropriate Domains would also include Chaos and Destruction.
Granted Power: The Dead Truce would be paramount if this is not
already required in the campaign some other way; Dead Inside would work
2nd: Ghoul Touch
3rd: Speak with Dead
4th: Blessed Forgetfulness (PSCS)
5th: Slay Living
6th: Antilife Shell
7th: Finger of Death
8th: Symbol of Death
9th: Power Word Kill
Death and Repose are natural Domains for priests of the Dead.
Fated Domain, Taker Domain
Granted Power: Extra Skills or Self-Sufficient, perhaps.
1st: Unseen Servant
2nd: Arcane Lock
3rd: Vampiric Touch
4th: Secure Shelter
5th: Secret Chest
7th: Instant Summons
9th: Summon Monster IX
Many Priests of the Fated would doubtless find reason to enjoy the Nobility Domain.
Fraternity of Order Domain, Guvner Domain
Granted Power: Intuit Pattern, regardless of other prerequisite (though what is a Guvner doing with less than Int 11?).
1st: Detect Law
2nd: Make Whole
4th: Discern Lies
6th: Analyze Dweomer
8th: Planar Union (PSCS)
There are many natural choices for clerics devoted to the philosophy
of the Fraternity: Law, the Mechanus Domain, Oracle, and Knowledge are
Free League Domain, Indep Domain
Granted Power: Faction-Free, Free Willed and Slippery are all good choices for the Indep Domain granted power.
2nd: Remove Paralysis
3rd: Celestial Refuge (PSCS)
4th: Freedom of Movement
5th: Break Enchantment
6th: Dispel Magic, Greater
7th: Ethereal Jaunt
8th: Spell Immunity, Greater
Zealous Indep clerics would very likely be attracted to the Liberation Domain.
Granted Power: Team Player.
3rd: Inspire Obedience (PSCS)
4th: Chain of Command, Lesser (PSCS)
5th: Telepathic Bond
6th: Chain of Command (PSCS)
7th: Hold Person, Mass
9th: Hold Monster, Mass
The peculiar juxtaposition of attraction for the Community and
Domination Domains is just another reason priests of the Harmony are
looked upon oddly by observers.
Granted Power: Justice Blow or Know Lies.
1st: Detect Evil
2nd: Zone of Truth
3rd: Glyph of Warding
4th: Phantasmal Killer
5th: Mark of Justice
9th: Power Word Kill
Whether a cleric of the Red Death is attracted to the Domains of
Law, Inquisition, or Death tends to say something significant about
their interpretation of the faction philosophy.
Revolutionary League Domain, Anarchist Domain
Granted Power: Slippery
1st: Protection from Law
2nd: Undetectable Alignment
4th: Detect Scrying
5th: Mage's Private Sanctum
Liberation would likely be a common domain for Anarchist clerics,
though Knowledge or Inquisition bespeaks an Anarchist truly dedicated to penetrating
the power structure's lies.
The Sign of One Domain, Signer Domain
Granted Power: Dreamer or Powers of Imagination would be good. The
ability to cast Conjuration (creation) spells at +1 caster level,
enjoying the same synergy with Artifice and Creation as those two
Domains already do, would also be interesting.
1st: Silent Image
2nd: Eagle's Splendor
3rd: Helping Hand
4th: Minor Creation
5th: Major Creation
6th: Programmed Image
7th: Limited Wish
8th: True Creation
Artifice and Creation, discussed above, would be good Domains themselves. Nobility is also a possibility.
Society of Sensation Domain, Sensate Domain
Granted Power: Alertness, Extraordinary Sense, and Sensory Touch are all excellent possibilities. So is a +1 to caster level for divination spells, stacking with the bonus from the Knowledge Domain.
2nd: See Invisibility
4th: Arcane Eye
5th: Prying Eyes
6th: True Seeing
7th: Arcane Sight, Greater
8th: Discern Location
Knowledge, Oracle and Inquisition are all useful for the inquiring Sensate.
Transcendent Order Domain, Cipher Domain
Granted Power: Cadence Whispers.
1st: True Strike
2nd: Cat's Grace
4th: Dimension Door
5th: Teleport (Divine Agility from Complete Divine appropriate)
6th: Find the Path
7th: Teleport, Greater
8th: Moment of Prescience
9th: Time Stop
Clerics of the Cadence would doubtless frequently manifest the Celerity, Luck, and possibly Oracle Domains.
Granted Power: Scramblespeak was the 2e defining ability of the
faction. Unlikely Event could also be an interesting granted power.
1st: Detect Chaos
3rd: Supremacy of the Passions
7th: Word of Chaos
8th: Cloak of Chaos
9th: Storm of Vengeance
Common Domains for clerics of the Xaositect philosophy would
certainly start with Chaos and Luck, with the Limbo planar Domain as
another common choice.
An interesting variant on the Xaositect Domain would be the
following: at the time of character creation, the GM rolls randomly to
choose one SRD spell of the appropriate level from among all spells he
decides are reasonably available: at the least, cleric and sorcerer
spells not in conflict with the player's alignment. These spells form
that player's Xaositect Domain. The character is aware of what each of
the spells is or could be.