I have massive, sweeping changes to Rogue and Monk, and plan on lesser changes to boost the other non-casters and nerfs to casters. But aside from that stuff, this is my current list of houserules:
[sblock]Races:
Dwarves: Stability is reduced to a +2, like the various improved combat maneuver feats have been. The Hardy bonus to saves is reduced to +1, and any APG replacement for Hardy may be subject to nerfing or banning.
Elves: Gain Fleet as a bonus feat.
Halflings: Lose Perception bonus and gain Low-light Vision. Racial feat allows them to gain Darkvision (60 ft).
Classes:
Barbarian: The con bonus from rage is factored into rounds/day. Rage can be maintained while unconscious, and the Barbarian can choose each round to retain it or end it even while unconscious. Roused Anger can be replaced for a new rage power (that you could have qualified for when you took Roused Anger) upon gaining Tireless Rage. The Barbarian's damage reduction from class is doubled when raging.
Bard: Fascinate uses perform check as the DC and each round of expended Perform usage grants up to 10 continuous rounds of Fascinate. Countersong and Distraction can likewise be maintained continuously for up to 10 rounds for each round of bardic music expended for the day. Ending any of these effects and starting them again consumes another round of music, as does prolonging the duration past 10/20/30/etc... rounds. A Bard may only get one free Suggestion attempt against any given creature per round expended on Fascinate. To try again within the same 10 round window, a round of performance for the day must be expended each time. Inspire Courage, Inspire Greatness, and Inspire Heroics' benefits linger for up to one round per 3 Bard levels after the performance is ended, though the duration of the lingering benefits cannot exceed the duration of the actual performance. Starting a new performance automatically ends any lingering musical effects. The 19th level ability of Jack of All Trades is removed.
Cleric: Let's try dropping them to d6 HD, see how that works.
Druid: See Cleric.
Fighter: Skill points increased to 4 + Int modifier per level. Gains Diplomacy, Knowledge (history), Knowledge (local), and Perception as class skills.
Inquisitor: An Inquisitor may select Point Blank Shot or any feat requiring Point Blank Shot as a bonus feat, in addition to choosing from Teamwork feats.
Monk: Needs so much help, it has its own topic.
Paladin: No changes.
Ranger: You may use the full Druid list when choosing your animal companion (still at level -3, though).
Rogue (all changes also apply to Ninja): Also needs so much help that it gets its own topic.
Wizard: Let's see how they survive at d4 HD. Sorceror can stay at d6.
Miscellaneous
All Spellcasters: Any of the spell-like abilities (typically of the 3 + casting mod times/day variety) gained by bloodline, arcane school, or domain are now Su abilities and thus do not provoke AoOs, among other things.
Evasion negates any effect entirely that normally has a half or partial effect on a successful Reflex save, not just damage. Improved Evasion causes the creature to suffer only the half or partial effect if he fails his saving throw.
Spellcasting:
Concentration
-Casting Defensively has a DC of 10 + 3*spell level
-While grappled, the DC to cast is 15 + 3* spell level. The DC when pinned is 25 +3*spell level. These replace factoring in the grappler's CMB at all.
Combat:
Combat maneuvers: Changing the modifiers for size to +/- 0/2/4/6/8, from the listed 0/1/2/4/8. Just seems more evenly distributed, and the modifiers close to medium are just way too minute.
Minimum Damage: Houseruling it to be a minimum of 1 damage (lethal or nonlethal, as the attack was originally) instead of 1 nonlethal damage. This still does not apply for DR, which CAN completely negate damage, only penalties on your damage roll (low str, cursed, silver weapon, etc...)
Hit Points: You die at -10 hp if you have a con score below 10.
Splash Weapons: These can inflict sneak attack damage with the primary hit, though not on the splash damage.
Skills:
Acrobatics: Only contains Balance and Tumble. No longer a Barbarian class skill. Can be used to roll on a landing (DC 15) to reduce falling damage by 10 ft (you can still also jump down with the Athletics skill, also). Without 3 Acrobatics ranks, if you stand in an area that requires balance checks, you lose your dexterity and dodge bonuses to AC. Tumble DCs follow 3.5's rules (ie, base DC 15 and so forth, no relation to CMD).
Athletics: New strength-based skill, combines Climb and Jump. Class skill for Barbarian, Bard, Druid, Fighter, Monk, Paladin, Ranger, Rogue (and Ninja), Antipaladin, Cavalier (and Samurai), Inquisitor, and Magus. Any character that would gain Climb as a class skill (such as through domain or mystery, etc...) gains Athletics as a class skill.
Diplomacy: DCs need to be addressed...
Escape Artist: You can use your Escape Artist modifier +10 instead of CMD to avoid a grapple.
Fly: Anyone can take ranks in the skill, whether you have magical or natural flight, or no means of flight at all.
Knowledges: For creatures that have advanced forms or are advanced HD versions of the base creature, you learn basic information relevant to all creatures of that type if you make the DC for the weakest possible specimen, just nothing specific to the threat before you. For example, if you made the DC for a wyrmling Red Dragon when encountering an Adult, you may learn about the fire immunity, breath weapon, etc..., but not traits the adult has that the wyrmling would not.
Perception: Now is "only" a combination of Spot and Listen and any other type of sensory reaction. Remains the best skill in the game, stop crying.
Sleight of Hand: Adding Search to its functions. Remains Dex-based. Elves and half-elves (and only them) retain the racial perception bonus on search checks with this new skill, since they had it in 3E. Renaming the skill, probably "Thievery" or similar.
Feats
Weapon Finesse: Any weapon that can be finessed can use the wielder's dexterity modifier instead of strength on attack rolls without need of this feat. This feat allows a creature to add his dexterity to damage with any light weapon or weapon with the finesse property instead of strength. You do not gain extra damage from wielding a weapon two-handed as you would with strength, and your damage is still modified by any strength penalty you may have (in addition to adding your dexterity modifier).[/sblock]
Incomplete, and other than the Athletics note hasn't really considered any of the new classes, though other than nerfing summoner and perhaps letting Inquisitor using his bonus teamwork feats on archery feats as well, not sure much needs to be done with the new classes anyway. Biggest area yet to be houseruled is spells. A LOT of them need to be nerfed.