Rating PrCs is difficult. It's obvious that some provide too much and some provide too little, but which is which depends on a lot of factors - base class entry being the most obvious. Where the difference between two "logical entries" is huge, those entries can be listed separately (see Rainbow Servant), but just like for base classes, a single PrC can go up or down based on optimization skill, and we should focus on what we see as the "average" use. We should only list a PrC multiple times if the multiple entries are all simple and straightforward given the requirements, as anything else falls under the individual's optimization skill.
It's also difficult to categorize power. Soulbow certainly adds more to Soulknives than Mindbender does to Sorcerers, but I think most will agree that a high level Mindbender will still beat a Soulbow with both arms tied behind its back. Still, ranking them that way is merely repeating the obvious, that some base classes are better than other, down through the list of PrCs ad nauseum. That's neither helpful nor productive. Instead, it would make more sense to rate PrCs by how much advantage they give, over their "logical entries". In other words, a PrC for Soulknives is held to a different standard than a PrC for Sorcerers, and the grade tells you how strongly you should consider taking that PrC, assuming you're already working on a build that could qualify.
So for this, I'll be referring to Tiers and how the PrC changes them, but I'm aware that there's multiple Tier systems out there that differ in substantial ways, and that some of these gradings will put classes into places they just don't belong when taken literally. A Tier 3 with an "up one" PrC wouldn't necessarily be a Tier 2, and a Tier 1 with a "down two" PrC would probably still be better than most Tier 3 classes. There will also be classes that go off the top or bottom of the scale. The goal is merely to make it clear that an "up two" is better than an "up one", and that both are only in reference to the starting point as given by the "logical entry". To repeat: the ranking is not literal. It's just a guideline to help novice or intermediate players know where to start looking.
Books included so far
[spoiler]Book of Exalted Deeds (ave: +0.182)
Book of Vile Darkness (ave: +0.647) - Samb
Champions of Ruin (ave: +0.0)- Tam_OConnor
Complete Adventurer
Complete Arcane - biznarf
Complete Divine
Complete Mage (ave: +0.545) - Surreal
Complete Psionic - Samb
Complete Scoundrel - Samb
Complete Warrior
Drow of the Underdark - Akalsaris
Dungeon Masters Guide (ave: -0.375)
Eberron Campaign Setting
Expanded Psionics Handbook (ave: +0.222)
Expedition to Castle Ravenloft
Expedition to the Deamonweb Pits - Zombieboots
Frostburn - tusk
Heroes of Horror (ave: +0.5)
Libris Mortis (ave: -1.0) - Salt_Crow
Lords of Madness (ave: +1)
Lost Empires of Faerun - Tam_OConnor
Magic of Incarnum - woodenbandman
Planar Handbook (ave: +0.0) - tusk
Player's Guide to Faerun (ave: -0.1) - Tam_OConnor
Races of Destiny (ave: +0.176) - tusk
Races of Eberron (ave: +0.625) - Salvonus
Races of Stone (ave: +0.467) - Surreal
Races of the Dragon (ave: +0.0) - tusk
Races of the Wild - CthulhuM and Sirek Inta
Sandstorm
Serpent Kingdoms (ave: -0.06) - Tam_OConnor
Stormwrack
Tome of Battle
Tome of Magic - jameswilliamogle
Unapproachable East (ave: +0.417) - Tam_OConnor
Underdark (ave: +0.333) - Tam_OConnor
[/spoiler]
Books still needed: Cityscape, Complete Champion, Draconomicon, Dragon Magic, Dungeonscape, Fiendish Codex II, Ghostwalk, Heroes of Battle, Miniatures Handbook, Shattered Gates of Slaughtergarde, and Weapons of Legacy, plus any setting-specific 3.5 books we've missed.
Up Two or More Tiers. These PrCs improve the power of their entry classes dramatically, either by building on strengths or by adding powerful new ones. Expect characters with these to blow their single-classed peers out of the water (and possibly get DM-smote, depending on the base class's power).
[spoiler]Anarchic Initiate
Anima Mage
Champion of Gwynharwyf
Disciple of Disapater
Dweomerkeeper
Emissaries of Barachiel
Halruuan Elder
Hulking Hurler
Initiate of the Sevenfold Veil (unless your DM overrules Veils blocking Antimagic Fields)
Incantatrix (when combined with other metamagic cost reducers)
Legendary Captain (if naval combat is required)
Moonspeaker (with Knowledge Devotion)
Necrocarnate (unless your DM limits what you can draw essentia from)
Planar Sheppard
Rainbow Servant (Warmage entry)
Runescarred Berserker
Sacred Exorcist (non-Cleric entry)
Sentinel of Bharrai
Shadowcraft Mage
Soulbow
Soul Eater
Sublime Chord
Tainted Scholar
Telflammar Shadowlord
Thrallherd
Thrall of Juiblex
Ur-Priest
Void Disciple
Walker in the Waste
Warshaper (non-casting entry)[/spoiler]
Up One Tier. These PrCs generally improve their entry classes substantially, without radically affecting game balance. Expect characters with these to be powerful allies or dangerous enemies, without totally overshadowing their single-classed peers.
[spoiler]Abjurant Champion
Abolisher
Acolyte of the Ego
Aglarondan Griffonrider
Annointed Knight
Arachnomancer
Arcane Heirophant
Ashworm Dragoon
Assassin
Atavist
Bear Warrior
Beloved of Valarian
Blackguard
Blade Bravo
Bloodclaw Master
Bloodhound
Breachgnome
Cabinet Trickster
Cavalier
Cavelord
Cancer Mage (broken with festering rage)
Celestial Mystic
Chaotician
Chameleon (an odd case by any standard)
Champion of Corellon Larethian
Church Inquisitor
Contemplative
Cragtop Archer
Daggerspell Shaper
Darkrunner
Death Delver
Deepwarden
Defender of Sealtiel
Demonwrecker
Dervish
Diabolist
Disciple of Amodeus
Disciple of Baalzebul
Disciple of Mephistopheles
Disciple of the Eye
Disciple of Thrym
Divine Crusader
Divine Oracle
Divine Prankster
Dragon Devotee (for non-casters)
Dragonmark Heir
Dread Fang of Lolth
Dread Pirate
Drow Judicator
Drunken Master
Earth Dreamer
Eldeen Ranger
Elemental Warrior
Elven High Mage
Enlightened Fist
Eternal Blade
Exotic Weapons Master
Eye of Horus-Re
Fatemaker (worse for bards)
Fatespinner (fifth level not recommended)
Fiend-Blooded
Fist of Raziel (Charging Smite paladin variant highly recommended)
Fleshwarper
Frenzied Berserker
Frost Mage (Sorc entry)
Ghost Faced Killer
Grey Guard
Halfling Outrider
Hammer of Moradin
Hathran
Heir of Siberys
Holy Liberator
Holy Scourge
Illithid Body Tamer
Illumine Soul
Initiate of the Sevenfold Veil
Ironsoul Forgemaster
Jade Phoenix Mage
Jaunter
Justicar of Tyr
Keeper of the Cerulean Sign
Knight of the Chalice
Knight of the Raven
Knight of Sacred Seal
Knight Protector
Leviathan Hunter
Lion of Talisid
Loredelver
Loremaster
Lyric Thaumaturge
Malconvoker
Mage of the Arcane Order
Magical Trickster
Master Inquisitive
Master of Many Forms (Ranger entry)
Master of Masks (Spellthief entry)
Master of Shadow
Master Specialist
Master Thrower
Menacing Brute
Mortal Hunter
Mountebank
Nentyar Hunter
Nightsong Enforcer
Nightmare Spinner
Noctumancer
Olin Gisir
Orc Warlord
Pale Master
Primeval
Prophet of Erathaol
Psibond Agent
Psionic Fist
Quori Nightmare
Radiant Servant of Pelor
Recaster
Rimefire Witch
Risen Martyr
Ruby Knight Vindicator
Runesmith
Sacred Exorcist (Cleric entry)
Sacred Fist
Sanctified Mind
Sand Shaper (Sorc entry)
Scion of Dantalion
Scion of Tem-Et-Nu
Scorpion Heritor
Sea Mother Whip
Shadowbane Inquisitor (in conjunction with Blackguard)
Shadowbane Stalker
Shadow Sentinal
Shining South
Shou Disciple
Singer of Concordance
Skypledged
Slayer
Slayer of Domiel
Spellfire Hierophant
Spellwarp Sniper
Stoneblessed
Suel Arcanamach
Temple Raider of Olidammara (for non-Rogue entry)
Thaumaturgist
Thayan Gladiator
Thrall of Demogoron
Topaz Guardian (gish entry)
Triadic Knight
Umbral Disciple
Unseen Seer
Urban Soul
Vassal of Bahamut
Vengeance Knight
Virtuoso
Warforged Juggernaut
War Mind (non-pure psi entries)
Warrior of Darkness
Warrior Skald
Weretouched Master
Whisperknife
Wild Plains Outrider
Wildrunner
Wild Soul
Winterhaunt of Iborighu
Witch Slayer (non-caster entry)
Zerth Cenobite[/spoiler]
Equal. These PrCs are roughly on par with their entry classes overall, trading strengths in certain areas for strengths in others, or provides moderate gains for a moderate investment (ie required feats or unfavorable multiclassing). Expect characters with these to fit naturally into a single-classed party.
[spoiler]Alienist
Animal Lord
Arcane Devotee
Archmage
Ardent Dilettant
Astral Dancer
Avenging Executioner
Battlerager
Battle Trickster
Beastmaster
Black Blood Hunter
Blood Magus
Champions of Valor
Child of the Night
Cipher Adept
Cloud Ancorite
Combat Trapper
Consecrated Harrier
Corrupt Avenger
Cultist of the Shattered Peak
Daggerspell Mage
Darkwood Stalker
Deep Diviner
Deepstone Sentinal
Disciple of Mammon
Disciple of the Word
Divine Champion
Divine Disciple
Divine Seeker
Dracolexi
Dwarven Defender
Dread Witch
Demonbinder
Ectopic Adept (but only if your DM uses CPsi nerfs already)
Eldritch Disciple
Eldritch Knight
Eldritch Theurge
Elemental Savant
Elocater (Psychic Warrior or Psychic Rogue entry)
Exorcist of the Sacred Flame
Eye of Gruumsh
Fang of Sseth
Fiendbinder
Flayerspawn Psychic
Frost Mage (Wizard entry)
Frost Rager
Fortune's Friend
Geometer
Gnome Giant-Slayer
Goliath Liberator
Great Rift Deep Defender
Great Rift Skyguard
Hand of the Adama
Highland Stalker
Imaskari Vengeance Taker
Inquisitor of the Drowning Goddess
Invisible Blade (feint not recommended)
Jordain Vizier
Justicar
Kensai
Knight of Iron Glacier
Knight of the Pearl
Knight of the Weave
Lord of Tides (Cleric Entry)
Luiren Marchwarden
Maester
Magelord
Maiden of Pain
Maquar Crusader
Master of Masks (general entry)
Master of Vipers
Mindspy (CAdv version)
Moonsea Skysentinel
Morninglord of Lathander
Nar Demonbinder
Nature's Warrior
Netherese Arcanist
Occult Slayer
Peregrine Runner
Pious Templar (except for 1 level dips)
Prime Underdark Guide
Psion Uncarnate
Purple Dragon Knight
Ravager
Reachrunner
Reforged
Red Wizard
Ronin
Ruathar
Runecaster
Sapphire Hierarch
Scar Enforcer
Scourge Maiden
Seeker of the Misty Isle
Serpent Slayer
Shaaryan Hunter
Shade Hunter
Shadow Adept
Shadowband Inquisitor
Shadowblade
Shadowcrafter
Shadowsmith
Shadow Thief of Amn
Soulcaster
Spellcarved Soldier
Spellsinger
Spinemeld Warrior
Spymaster
Stonedeath Assassin
Stonelord
Stonespeaker Guardian
Stormcaster
Storm Disciple (Ardent dip entry)
Stormlord
Stormsinger
Stormtalon (except for 1 level dips)
Streetfighter
Sword of Righteousness
Talontar Blightlord
Tattooed Monk
Temple Raider of Olidammara (Rogue entry)
Thayan Slaver
Totem Rager
Thayan Knight
Thrall of Orcus
Ultimate Magus (except with fast entry tricks)
Uncanny Trickster
Unseen Seer
Vermin Keeper
Vigilante
War Chanter
War Mind (pure PsiWar entry)
Warshaper (casting entry)
Warsling Sniper
Wild Mage
Witch Slayer (gish entry)
Zhentarim Spy[/spoiler]
Down One. These PrCs are generally inferior to their obvious entry classes, losing out on important features in order to gain things that are likely not to matter in the long run. Expect characters with these to struggle in a single-classed party. They may still be viable for cherrypicking, or under heavy optimization.
[spoiler]Ancient Master
Arachnomancer
Arcane Trickster
Argent Savant
Bladesinger
Black Blood Cultist
Black Flame Zealot
Bloodstorm Blade (except 2 level dips)
Cavestalker (Ranger entry)
Celebrant of Sharess
Cerebremancer
Cloaked Dancer
Cognition Thief
Coiled Cultist
Cryokineticist
Dark Hunter
Death's Chosen
Demonlogist
Doomguard
Dragon Disciple
Dragonheart Mage
Dungeon Delver
Durthan
Ebon Saint
Effigy Master
Elocater (Psion entry)
Enlightened Spirit
Exalted Arcanist
Exemplar
Extreme Explorer
Evereskan Tomb Guardian
Geomancer (varies greatly on entry)
Glorious Servitor
Halruuan Magehand
Harper Agent
Harper Paragon
Heirophant
Horizon Walker
Hospitaler
Hunter of the Dead
Incandescent Champion
Initiate of Pistis Sophia
Justice of Weald and Woe
Kinstalker
Lord of Tides (Druid Entry)
Luckstealer
Martyred Champion of Ilmater
Master of Many Forms (Druid entry)
Master of Nine (unless you can get some of the feats for "free")
Master of Radiance
Master of Shrounds
Master of the Yuirwood
Master Transmogrifist
Mindspy (CWarrior version)
Monk of the Long Death
Mystic Theurge
Naga Lord
Nightmask Deathbringer
Nightsong Infiltrator
Order of the Bow Initiate
Outcast Champion
Purifier of the Hallowed Doctrine
Pyrokineticist
Rage Mage
Rainbow Servant (Sor/Wiz entry)
Sacred Purifier
Sand Shaper (Wiz Entry)
Scarlet Corsair (except with capstone abuse)
Sea Witch
Shadowdancer
Shadow Sun Ninja (unless you resist Con damage)
Shining Blade
Skylord
Slime Lord
Spellguard of Silverymoon
Spellsword (except for 1 level dips)
Stalker of Kharash
Storm Disciple (Pure Ardent entry)
Sunmaster
Swanmay
Tempest
Tenebrous Apostate
Thief-Acrobat
Thrall of Graz'zt
Topaz Guardian (caster entry)
Troubadour of Stars
Vermin Lord
Visionary Seeker
Warpriest
Wayfarer Guide (except for 1 level dips)
Yathchol Webrider[/spoiler]
Down Two or More Tiers. These PrCs completely fail to do what they were trying to do, or makes heavy sacrifices for little to no gain. Expect characters with these to be unplayable without heavy optimization effort, or some cunning trick.
[spoiler]Acolyte of the skin
Apostle of Peace (not broken, but blatantly contradictory text on material possessions)
Arcane Archer
Bereft
Blighter
Brimstone Speaker
Cavestalker (Druid entry)
Defiant
Dirgesinger
Duelist
Entropomancer
Evangelist
Eye of Lolth
Fochlucan Lyrist (unless Evasion is gained without dips, then Up One Tier)
Green Star Adept
Incarnum Blade
Insidious Corrupter (Arcane Spellcaster entry)
Lifedrinker
Master of the Unseen Hand
Metamind (higher with abuse of the capstone)
Mindbender (except for 1 level dips)
Ollam
Reaping Mauler
True Necromancer
Wavekeeper
Witchborn Binder
Wonderworker
Yathrinshee[/spoiler]
Note - possible reorganization coming.