Toughness
While tempting to some, fact is that by level 10, those 3hp are going to seem like a waste of a feat. To remedy this, Toughness will now provide 1 bonus HP per level. This balances it better with other feats that act as an effective +2 to a stat for one single purpose. This also means the feat can only be taken once, however.
Knowledge and Monsters
While I would like to reduce metagaming, there's quite simply no way I can really enforce that short of going to absurd lengths like "Haha, nice try, but the blue icicle covered troll is immune to fire!" and I don't think any of us want to go down that road.
So, I only ask that you consider what makes sense for your character to really know when it comes to monster strengths and weaknesses. Conversely, if I use a monster you're unfamiliar with but you think your character should know about, you can request to make a knowledge check (I'll tell you the relevant subtype) and then I'll give you information depending on the DC you beat - I won't ever give wrong information for failing that check, though.
Sorcerors
Get Eschew Materials for free at first level. Do I even have to explain this one?
Druids and Rangers
Animal Companion progression is swapped between these two classes - ie, Rangers get full progression and Druids get half.
Wizard Spells at Level Up
When a Wizard levels up, rather than being able to put 2 new spells in her spellbook for free, she can instead get any number of spells so long as the combined level of those spells is equal to 2 times the highest level she can cast.
Example
Alveria the Wizard hits level 9, gaining the ability to cast 5th level spells. She can now immediately add two 5th level spells to her spellbook. Alternatively, she could add one 2nd level, one 3rd level, and one 5th level spell. Or ten 1st level spells if that took her fancy.
Energy Drain
Energy Drain will never result in actual lost levels. However, if the fort save made after 24 hours fails, the negative level condition becomes permanent until removed via a Restoration spell or similar.
Stabilising
When reduced to below 0 hp, a percentile roll must be made each round to stabilise or lose further hp. The target of this roll is equal to the character's constitution score or lower.
Weapon Changes
Flail: has a threat range of 19-20.
Damage Reduction and Special Materials
Cold Iron no longer exists. Normal metal weapons count as Cold Iron for bypassing damage reduction of that type.
Alchemical Silver does not do any less damage than normal metal.