[Note that not all of the following modifiers are likely to come up in initial playtest. Some I include here only to show how I plan to change (or not to change) how to handle the modifier types when they do come up.]
Ability Modifier
Ability modifiers apply to die rolls for character actions involving the corresponding abilities.
Adaptation modifier
An adaptation bonus (or penalty) applies when a creature’s body is especially well-suited (or ill-suited) to some task.
Alchemical Bonus (NYIP)
An alchemical bonus is granted by the use of a nonmagical, alchemical substance such as antitoxin.
Circumstance Modifier
A circumstance bonus (or penalty) arises from specific conditional factors impacting the success of the task at hand. Circumstance bonuses stack with all other bonuses, including other circumstance bonuses, unless they arise from essentially the same source.
Competence Modifier (NYIP I think, since it applies to bonuses bestowed by magic etc rather than normal skill)
A competence bonus (or penalty) affects a character's performance of a particular task, as in the case of the bardic ability to inspire competence. Such a bonus may apply on attack rolls, saving throws, skill checks, caster level checks, or any other checks to which a bonus relating to level or skill ranks would normally apply. It does not apply on ability checks, damage rolls, initiative checks, or other rolls that aren't related to a character's level or skill ranks. Multiple competence bonuses don't stack; only the highest bonus applies.
Deflection Bonus (NYIP)
A deflection bonus affects Evasion and is granted by a spell or magic effect that makes attacks veer off harmlessly. Deflection bonuses stack with all other bonuses to Evasion except other deflection bonuses.
Dodge Bonus
A dodge bonus improves Evasion, resulting from physical skill at avoiding blows and other ill effects. Dodge bonuses are never granted by spells or magic items. A Dexterity bonus to Evasion is a dodge bonus; any rule to the effect that a situation or effect negates a character's Dexterity bonus also means that you lose any other dodge bonuses you may have as well (exception: wearing armor may limit your Dexterity bonus; it does not affect other dodge bonuses). Dodge bonuses stack with all other bonuses to Evasion, even other dodge bonuses.
Enhancement Bonus (NYIP I think)
An enhancement bonus represents an increase in the sturdiness and/or effectiveness of armor or natural armor, or the effectiveness of a weapon, or a general bonus to an ability score. Multiple enhancement bonuses on the same object (in the case of armor and weapons), creature (in the case of natural armor), or ability score do not stack. Only the highest enhancement bonus applies. Enhancement bonuses are subject to the rules of the quantity they enhance – for example, enhancement bonuses to armor DR or natural armor DR do not apply against immaterial attacks, because armor and natural armor do not protect against immaterial attacks [immaterial attacks, AKA incorporeal, are NYIP but I retain the example to show the rule hasn’t changed].
Insight Bonus (NYIP)
An insight bonus improves performance of a given activity by granting the character an almost precognitive knowledge of what might occur. Multiple insight bonuses on the same character or object do not stack. Only the highest insight bonus applies.
Instinct bonus
An instinct bonus is granted when a creature has an instinctive behaviour (rather than learned skill) that aids it in some task.
Luck Modifier (NYIP)
A luck modifier represents a special source of good (or bad) fortune. Multiple luck bonuses on the same character or object do not stack. Only the highest luck bonus applies.
Morale Modifier
A morale bonus represents the effects of greater hope, courage, and determination (or hopelessness, cowardice, and despair in the case of a morale penalty). Multiple morale bonuses on the same character do not stack. Only the highest morale bonus applies. Nonintelligent creatures (creatures with an Intelligence modifier of -5 or no Intelligence at all) cannot benefit from morale bonuses.
Resistance Bonus (NYIP)
A resistance bonus affects saving throws, providing extra protection against harm. Multiple resistance bonuses on the same character or object do not stack. Only the highest resistance bonus applies.
Size Modifier
A size bonus or penalty is derived from a creature's size category. Size modifiers of different kinds apply to Evasion, attack rolls, Hide checks, grapple checks, and various other checks.