In D&D 3.5e, do ability modifiers apply to all skills, or do they only apply to skills that you've spent skill points putting ranks into? The way the rulebook explains it is a bit confusing.
Ability modifiers apply to all skills even if you haven't trained in them. If your dexterity modifier is +5, all your dexterity-based skills have an ability modifier of +5 - you just have a natural aptitude at these skills.
Someone who's strong, for instance, is just naturally good at climbing, and gets their strength bonus to climbing checks even if they've never trained in it. Likewise, someone who's very charismatic is just naturally good at diplomacy and intimidation.
That said, some skills - such as Disable Device - are trained only, and cannot be used if you're untrained in them. For these ones, your natural aptitude at them won't matter until you've trained in them, because you simply won't be able to use them.