Apart from this there isn't much more to these saves, except saves executed in spells, as per below!
Saving Throw Bonuses vs Spells
There are four main ways to gain a saving throw bonus vs. spells - the spell Protection from Spells which adds +8 against spells only (items may also provide similar bonuses), Dwarf's feat Hardiness vs. Spells, the Arcane Defence line of feats, and Spellcraft.
Bug note: This is bugged and only applies when the saving throw vs. spells is implicit.
Spellcraft has a built in bonus to saving throws; SPELLCRAFT_NUM_RANKS_PER_SAVE_BONUS is usually 5 which means that you get +1 vs. Spells for each 5 ranks, making Sorcerers and Wizards (and usually Clerics, Druids) inherently quite defensively minded when it comes to enemy spells.
If you have 0 ranks in Spellcraft from levelling (ie untrained) you cannot gain a bonus or penalty from this - even if you apply a +50 bonus SKILL_SPELLCRAFT as an effect. Once you have 1 rank of spellcraft you can apply bonuses to it and they'll apply, so any temporary bonuses from items or effects also apply to the generated complete value (as long as you have 1 rank to begin with).
The way this bonus works is in these ways:Spellcraft has a notable bug: any spell script will trigger the bonus from spellcraft OR when the saving throw type is SAVING_THROW_TYPE_VS_SPELLS. This means it applies to items like, say, Wine/Beer/Sprits, or Garlic as well as all monster and feat abilities such as Harper: Sleep and so on, ie anything with impact scripts.
Things that explicitly specify SAVING_THROW_TYPE_SPELL - this is only used really to be explicit for Ruin and Hellball - which since they are UserType of 2 already apply the bonus! Odd eh?
EG: A Wizard casting Daze causes it to occur, as would a but Harper " casting " their Sleep Feat. A Gaze: Confusion would trigger it as wellthe feat Sleep would not. Spellabilities also have this bonus applied, such as Gaze: Confusion.
NOTE: as mentioned above Spellcraft applies to all sources of spells.2da script calls due to bugs. This is only relevant for the feat and effect bonuses.
However this will not apply outside of the base original spell script, meaning: