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.
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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, Appraise, or Knowledge - are trained only. Some like Disable Device cannot be used at all if you're untrained in them, whilst for others like Appraise and Knowledge, you can only do a limited amount without training (e.g. you can't do an untrained Knowledge check for over DC 10). For these ones, your natural aptitude at them won't matter much until you've trained in them, because your character simply can't do most of this stuff.