I've seen a few things that interact with certain bonuses.
examples: Fate's Favored for Luck; Courageous weapon for Moral.
Are there any other feats/abilities/spells out there that effect specific bonus types?
Lots of them.
thanks...
For morale bonuses, I like Moment of Greatness, which doubles them for each character once. So, nearly all parties have access to Bless or Flagbearer right from 1st level, and this makes those +2 instead of +1 (at least for one roll). Later, go with Heroism or Good Hope that are +2 and get doubled to +4 with the Moment of Greatness.
I later took Encouraging Spell to make my Good Hope a +3 morale bonus, for a 4th level Bard slot. I do have to pre-cast it with an Extend Rod to get around the 1 round spontaneous casting time when using Encouraging though. It's obviously better if you have a party cleric cast the Moment of Greatness with a +3 Good Hope spell than with a +1 Bless, in terms of the numbers (+3 doubles to an impressive +6) and in terms of the action economy (1 round pre-buff between 2 characters, instead of 2 rounds of actions for the bard).
Note also, Suppress Charms and Compulsions has 1 option for a +4 morale bonus on saves, and that doubles to +8 for 1 save with the Moment of Greatness, so against charms and dominations, that's a better action than Good Hope against some opponents.
If you are human (or count as human, for half-breeds and certain outsiders), then you can take the Imperious Sorcerer Bloodline. It's 3rd level ability, Heroic Echo, increases all competence and morale bonuses you gain by 1, similar to Fate's Favored. You can get this on any character via VMC or Eldritch Heritage. It also works wonders with a Pale Green Prism Ioun stone.