You may or may not agree with this, but the following are a number of general miscellaneous tweaks I've made to the rules for my games. This list will be constantly expanding and growing for quite a while.

Improving in Ability Scores (pg. 29) changes: Stats are gained every third level, not every fourth. (Thanks to The Shocel for this idea)

Armiger (pg. 38) Armor Tokens: The Armiger starts with a number of Armor Tokens equal to the DR rating of the armor he is wearing. (potential rule pending playtesting results)

Armiger (pg. 38) Gains bonus feats from the Armor category at 2/6/10/14/18, a la Archer Projectile feats. (potential rule pending playtesting results)

Berserker (pg. 41): DR changed to 1dX/magic.

Weapon Master (pg. 65) weapon token pool: dual wield sacrifice focus on either of their weapons particularly, and therefore set their token generation at 1/hit from 1-10 and 2/hit from 11-20. (thanks to Huiyin for this idea)

Multiclassing (pg. 72) feat mastery formula: Highest Mastery + Half all other masteries

Concentration (pg. 84) Casting defensively: DC 25.

Knowledge (pg. 98) Extended Skill check: Replaced by the Research skill. (More specific to my campaign than a general rule)

Speak Language (pg. 105): Changed to add levels of fluency in written and spoken knowledge. (More specific to my campaign than a general rule)

Improved Unarmed Strike (pg. 116): The damage die is raised by size category, IE 1d3 -> 1d4 for medium sized creatures.

Rapid Reload Mastery 1 (pg. 140) changed to Hand and Light: Free, Heavy: Move.

Unarmed Strike (pg. 161) descriptor: Without I.U.S. – power if Str is higher, finesse if Dex is higher, With I.U.S. – May switch between power and finesse as a free action once per round or as dictated by your unarmed combat style.

Ready (pg. 177) is no longer a Free Action but is now a Standard Action as per core 3.5 (Possibly change it to a swift action).