See also: Character Combat
The term "Stacking" means combining for a cumulative effect. It refers to modifiers (bonuses and penalties) that combine instead of replacing one another.
Generally, factors that apply modifiers to a statistic, roll, or check combine if they have different descriptors. For example, a competence bonus of +2 is used instead of a competence bonus of +1 when both bonuses are applied to the same statistic, roll, or check.
Any bonus without a descriptor (sometimes called an "unnamed bonus") stacks with all other bonuses, including bonuses without a descriptor.
The only descriptor bonuses that stack with others of the same type are circumstance bonuses and dodge bonuses. (Even then, circumstance bonuses stack only if they're not provided by essentially the same circumstances.)
Other descriptor bonuses do not stack with others of the same type unless specifically noted otherwise.
All penalties stack regardless of source.