So here are my few comments for now...
Classes:
PHB II: Knight, Beguiler, Dragon Shaman, Duskblade; all cool and acceptable within the realm of the Eberron world. I don't particularly agree with making the Knight's challenge ability supernatural, sure it doesn't always make sense, but oh well, I don't think it's going to break the game and I think the more house rules the more difficult things become. I really want to play a Beguiler
Complete Books: Scout, Spellthief, Warlock, Spirit Shaman, Swashbuckler, Hexblade, Ardent, Lurk, Divine Mind. All of those, sure, good with me. The war mage I could toss either way really. I despise the favored soul cause it stomps the poor life out of the sorcerer comparably (all good saves, special abilities, more spells known) not cool. Swashbuckler, while it doesn't make me dance for joy and does encourage dipping for three levels, at least lets a character play a lightly armored warrior with decent skill points.
Races of Books: Allowing the racial substitution levels from Races of Eberron is agitating in that only the Eberron races get those nice handy customizations that are quite cool from the other Races books. Perhaps we should either make our own racial substitutions that are Eberron focused or use the ones from the Races books.
Heroes of Horror: Archivist is very cool and makes a ton of sense in the Eberron setting.
Magic of Incarnum: Burn the book, doesn't fit at all.
Tome of Magic: Binders are cool, the rest ditch it.
Spells & Powers:
Orb spells... if you make them SR yes, give them something a little more.
Spikes & brambles... the bonus was changed to an enhancement bonus to damage, so they no longer stack, let 'em in. I've never seen it abused except at high near epic levels.
Wraithstrike... limit it to your next melee attack this round. Then create a greater version (level 3 or 4) which does what the normal one does.
Spell Compendium: let it in, but require the spells to be found if not a spontaneous caster.
Complete Psionic: use the new powers but perhaps neglect the changes it made to prior powers that weren't put into normal errata for the XPH.
Feats:
Complete Divine: Divine Metamagic (put the restriction the Incantatrix has so that you must be able to normally cast the metamagiced version), Disciple of the Sun (perhaps instead of a turn attempt require an action point or 2 to be spent).
Complete Arcane: The spell-like ability feats make the Dragonmarked feats pale in comparison partly, usually granting three spells for one feat, compared to one spell. Remove the Sudden Metamagic feats. Change the Double Wand Wielder feat to say instead of just expending 2 charges instead of 1, doubling the number of charges expended through it.
Complete Adventurer: Really, I'd rather see some feat abilities get folded into skills to make them more useful rather than requiring a feat on them (Goad, Extraordinary Concentration & Spell Aim, Appraise Magic Value, Disguise Spell, Hear the Unseen, Improved Diversion)