House Rules

Allowed Classes
The big one: no spellcasting or similar (manifesting, soul binding, etc) classes, except incarnum classes (and see below).

From the SRD:
The Barbarian, Fighter, Monk, Rogue and variants (UA, etc) are all OK.
The Paladin and Ranger are OK with non-spellcasting variants (such as the ones from Complete Warrior or Complete Champion).

Magic of Incarnum
Of course, the Incarnate, Soulborn and Totemist are all good.

Completes
The Scout, Ninja, Samurai and Swashbuckler are appropriate.

Tome of Battle
Crusader, Swordsage, Warblade: all good.

Other
Knight, Marshal, anything without casting or casting-like abilities.

Classes

Soulborn
The Soulborn's bonus feat list is extended to include Expanded Soulmeld Capacity, Improved Essentia Capacity, Open Chakra and Shape Soulmeld

Sapphire Hierach
You no longer need spellcasting to get into the Sapphire Hierach PrC; instead, it grants it. Further, the class is generalised to cover any alignment.

Prerequisites
Alignment: Any except True Neutral
Skills: Knowledge (arcana) 6, Knowledge (religion) 6
Meldshaping: 3 soulmelds
Essentia: 3
Deity: Must provide Law, Good, Chaos or Evil domain.

Code:

L1:  Spellcasting, Alignment, Turn/Rebuke Undead, Consultation 1/level
L2:  +1 spells, +1 melds, Domain spells
L3:  +1 spells, +1 melds, Smite Opposition 1/day
L4:  +1 spells, Domain power, Consultation 3/level
L5:  +1 spells, +1 melds, Saves: +4 vs oppsotion, DR 1/opposition
L6:  +1 spells, +1 melds, Smite Opposition 2/day
L7:  +1 spells, Sapphire Body (25%), DR 2/opposition
L8:  +1 spells, +1 melds, Smite Opposition 3/day
L9:  +1 spells, +1 melds, Timeless Body, DR 3/opposition
L10: +1 spells, +1 melds, Sapphire Body (50%), Consultation 1/month

Alignment: Pick Lawful, Chaotic, Good or Evil. You must be of this alignment and your deity must grant this domain. All your Sapphire Hierach class features work off this alignment. For example, if you are Chaotic Evil, and choose Chaotic, Smite Opposition smites only Law, not Good.
Spellcasting: You gain spells like a Cleric of your level. You are considered to have the Law, Chaos, Good or Evil domain (as appropriate). You get bonus spells and an increase to save DCs based on Wis.
Turn/Rebuke Undead: As a Cleric of your level.

Soulcaster
You no longer need spellcasting to get into the Soulcaster PrC; instead, it grants it.

Prerequisites
Skills: Knowledge (arcana) 6, Spellcraft 6, Concentration 2
Feats: Incarnum Spellshaping
Meldshaping: 3 soulmelds, 1 chakra bind

Code:

L1:  Spellcasting, +1 melds
L2:  +1 spells, +1 melds
L3:  +1 spells, Arcane Investment 1
L4:  +1 spells, +1 melds
L5:  +1 spells, Chakra binds (crown, feet, hands)
L6:  +1 spells, +1 melds
L7:  +1 spells, +1 melds
L8:  +1 spells, +1 melds, Arcane Investment 2
L9:  +1 spells, Chakra binds (arms, brow, shoulders)
L10: +1 spells, +1 melds, Magical Distillation

Spellcasting: You gain spells like a Sorcerer of your level. You get bonus spells and an increase to save DCs based on Cha.

Soul Manifester
You no longer need manifesting to get into the Soul Manifester PrC; instead, it grants it.

Prerequisites
Skills: Knowledge (arcana) 6, Concentration 6, Spellcraft 2
Feats: Azure Talent
Meldshaping: 3 soulmelds, 1 chakra bind

Code:

L1:  Manifesting
L2:  +1 manifesting, +1 melds
L3:  +1 manifesting, +1 melds, Psionic Investment 1
L4:  +1 manifesting, +1 melds
L5:  +1 manifesting, Chakra binds (crown, feet, hands)
L6:  +1 manifesting, +1 melds
L7:  +1 manifesting, +1 melds
L7:  +1 manifesting, +1 melds, Psionic Investment 2
L7:  +1 manifesting, Chakra binds (arms, brow, shoulders)
L7:  +1 manifesting, +1 melds, Psionic Distillation

Manifesting: You gain power points and powers like a Psion of your level. You get bonus power points and an increase to save DCs based on Cha.

Feats

Azure Talent: You do not have to be Psionic to take this feat. In fact, doing so makes you Psionic.
The PP granted by each point of essentia increases by 1 for each point of essentia invested - so instead of getting 2PP for 1E, 4PP for 2, etc, you get 2PP for 1, 5PP for 2, 9PP for 3, etc.
So long as at least 1 point of essentia is invested in it, this feat also allows you to use a single 1st-level power (chosen when taking the feat) with manifester level equal to twice the invested essentia, less 1. You use Cha as your key stat.
If you gain the ability to manifest powers from another source (i.e. Soul Manifester), you use your manifesting level from that source if it's higher.
This replaces Wild Talent and Hidden Talent.

Incarnum Spellshaping: Once per day you may invest essentia into this feat and choose a number of incarnum spells to prepare. You may prepare one spell level for the first point of essentia, two for the second, three for the third, and so on (these stack) and cast each of these once that day. Your caster level is equal to the twice the amount of essentia invested, less 1 (1=1, 2=3, 3=5, etc), and Cha is your key stat.
If you gain the ability to cast spells from another source (i.e. Soulcaster) they may be treated as spells from that source (same caster level if higher, etc).

Open Chakra: You can always bind a soulmeld to the opened chakra, regardless of any chakra binds you may or may not have from a meldshaping class.

Psycarnum Infusion: I'm going to stomp on abusing this with certain incarnum feats. If you use it with Azure Talent, the PP is not temporary so you can't choose to spend it first - thus, you lose PP again as soon as you stop using Psynarnum Infusion. You can use it with Incarnum Spellshaping or Midnight Metamagic, but once the spells are chosen they can't be changed and once they're cast, that's it, reinvesting the essentia doesn't give you more.

Shape Soulmeld: If you can already shape soulmelds, the soulmeld you get from this feat remains separate, and is always shape-able regardless of your other meldshaping limits. However, the maximum number of soulmelds is limited by your Con.

Scribe Scroll/Imprint Stone/Craft Staff: Do not exist.

Brew Potion/Craft Wondrous Item/Craft Magical Arms and Armour/Forge Ring: See "Crafting", below.

Full Transparency
Unless an effect is specific to spells, powers, soulmelds etc (DM's discretion), it applies to all such things. This is an extension of Psionic/Magic transparency; now, Psionics and typical Magic are now considered Incarnum for these purposes.

Psicraft is now part of Spellcraft.

Use Psionic Device is now part of Use Magic Device.

Knowledge (Psionics) no longer exists - replace any bonuses/requirements/etc with Knowledge (Arcana).

Craft Psionic Arms and Armour is now part of Craft Magical Arms and Armour (see "Crafting", below).

Crafting Magic Items
Since spells and powers will be available to very few people and even then, they will be quite restricted, a crafting overhaul is in order. Thus, I'm going for a more Pathfinder-like approach.

Brew Potion
Requirements: Changed to Manifester Level 1, or Craft (Alchemy) 4 ranks.
Brewing potions is now considered an alchemical process. To brew a potion, you make a Craft (Alchemy) check against a DC of 13 + spell level + caster level. If you fail the check, you use up half your materials (so 1/4 the base price) and the time spent. You gain a +2 synergy bonus on this check if you have 5 ranks or more in Spellcraft.
There is no XP cost to brewing potions.
Special: A Potion of Cure Light Wounds (CL1) has a DC of only 13.

Craft Wondrous Item/Craft Magic Arms and Armour/Forge Ring
Requirements: Any Caster Level requirement is replaced with a Meldshaper Level one. Forge Ring specifically only requires an ML of 7.
To craft an item you must make a Spellcraft check halfway through the process, or lose half your materials (so 1/4 the base price) and any progress you've made on the item. The DC is 5 + item's caster level. Further, you can make an item without the required spells by raising the DC by 4 per spell, or without other requirements by raising the DC by 6 per requirement.
You gain a synergy bonus appropriate to the type of item:
Amulet/Ring - Craft (Jewellery)
Armour - Craft (Armourworking)
Weapon - Craft (Bowmaking or Weaponsmithing)

Craft Wand
Unchanged, except there is no XP cost.