A thief gets a bonus to 'sneak' (what I'm calling the unified ability for move silent, hide in shadows, and assorted similar abilities) equal to level +2. A level 10 thief rolls d20 +12 (target 20) to sneak successfully. Boots of elvenkind or a cloak of elvenkind give +10 to sneak (and the two together give +15). A stoutling (re-skinned halfling) gets +6 to sneak while outdoors (but it never improves).
A thief also gets a bonus to 'spot' (the unified ability to find secret doors, traps, hidden objects, etc.) equal to level +2. A level 7 thief rolls d20 +9 (target 20) to spot a secret door or a trap. Elves get a bonus of +4 to spot while outdoors; dwarves get +4 to spot while underground.
A cleric rolls d20 to turn undead, added his/her wisdom modifier as a base. The target starts as 10 for an undead of the same level as the cleric. For each level (HD) difference between the cleric and undead, the target moves by 3; a cleric 5 attempting to turn a 7 HD vampire needs a 16 or better to turn.
I am leaning towards take the suggestion of +Aaron Day to tie all saving throws to your prime requisite. At first I wasn't big on this, but the more I think about it the more I like it. The fighter uses his great strength to hold up his shield against the dragon breath, fight off the mind control, shake off the poison effect, and even to smack away a fireball with his two-handed sword. It's got a great epic feel to it. The magic user wields his powerful intellect to know exactly where to pinch his arm to stop the poison from getting into his bloodstream, he knows exactly how to inhale to minimize the impact of the poison gas, and he correctly determines how to avert his gaze to prevent the basilisk from turning him to stone.