Sources of holy damage:
• Spells:
- Blessing of the Righteous (Player's Handbook II)
• Feats:
- Holy Ki Strike (Book of Exalted Deeds)
- Nemesis (Book of Exalted Deeds)
- Sanctify Natural Attack (Book of Exalted Deeds)
- Sanctify Weapon (Book of Exalted Deeds)
• Classes:
- Demonwrecker (Expedition to the Demonweb Pits)
• Salient Divine Abilities:
- Divine Storm (Deities and Demigods)
- Energy Storm (Deities and Demigods)
• Weapon Special Abilities:
- Holy (Dungeon Master's Guide + Book of Exalted Deeds)
- Holy Surge (Dungeon Master's Guide II)
• Special abilities:
- Smite Evil (Player's Handbook + Book of Exalted Deeds)
• Monsters:
- Zaphkiel, the Watcher (Book of Exalted Deeds)
• Templates:
- Saint (Book of Exalted Deeds)
• Materials:
- Kuni Crystal (Oriental Adventures)
Sources of unholy damage:
• Spells:
- Black Bag (Book of Vile Darkness)
- Damning Darkness (Lords of Madness)
- Pulse of Hate (Book of Vile Darkness)
• Feats:
- Corrupt Spell (Book of Vile Darkness)
- Corrupt Spell-Like Ability (Book of Vile Darkness)
- Hellsworn (Exemplars of Evil)
• Classes:
- Diabolist (Book of Vile Darkness)
- Knight of the Skull (Dragonlance Campaign Setting)
• Domains:
- Entropy (Fiendish Codex I)
• Weapon Special Abilities:
- Unholy (Dungeon Master's Guide + Arms and Equipment Guide)
- Unholy Surge (Dungeon Master's Guide II)
• Items:
- The Regalia of Evil (Arms and Equipment Guide)
• Monsters:
- The Dread Emperor (Book of Vile Darkness)
- Mephistopheles, Lord of the Eighth (Book of Vile Darkness)
• Places:
- Pit of Many Colors (Champions of Ruin)
There is a link between holy/unholy damage and holy/unholy weapons, in the dungeon master's guide 3.5 it only says "extra damage" but on some handbooks (Arms and Equipment Guide, Book of Exalted Deeds) it is said that damage is holy/unholy.
There are no general rules for holy/unholy damage, the specific ruling of each source must be followed.
There is no good/evil damage. There is damage reduction against good-aligned or evil-aligned weapons, but is has nothing to do with the weapon dealing good damage, weapons can only do piercing, slashing or bludgeoning damage. It's like damage reduction against specific materials, silver weapons don't do "silver damage".
A lot of the sources are located in the Book of Vile Darkness and Book of Exalted Deeds, but not all of them, one of them is from the Lords of Madness for example.