What do these D&D bonuses do?

I think those are both somewhat general terms; they're describing the source of various bonuses, rather than their exact effect. The item or spell (etc) giving the bonus should describe exactly what they apply to. For example, the "Stone of Good Luck" gives +1 to saving throws, ability checks, and skill checks, whereas the Luck Blade gives a +1 to saving throws only. Likewise the effects of various morale bonuses and penalties vary: For example, a bard's Inspire Courage effect grants a a +1 morale bonus on saving throws against charm and fear effects and a +1 morale bonus on attack and weapon damage rolls. On the other hand, the Bless spell gives a +1 morale bonus on attack rolls and on saving throws against fear effects.