There are a number of different permanent abilities besides the normal perks that you can get:
There are the 13 guardian stones, found at locations throughout the world:
- Warrior: Combat skills increase 20% faster
- Thief: Stealth skills increase 20% faster
- Mage: Magic skills improve 20% faster
- Lover: All skills improve 15% faster
- Apprentice: 2x magicka regeneration, twice as vulnerable to magic
- Atronach: +50 magicka, 50% magic absorb, -50% magicka regeneration
- Lady: +25% health and stamina regeneration
- Lord: +50 damage resist, 25% magic resist
- Ritual: All dead things around you become undead and fight for you
- Serpent: Attacks have a chance to paralyze targets for 5 seconds and 25 damage
- Shadow: 60 second invisibility power
- Steed: +100 weight capacity, no movement penalty from armor
- Tower: You can unlock one expert-level or lower locked door/chest per day without lockpicks
These are mutually exclusive: you can only have one active at any time.
There are a few permanent abilities you get as a result of completing various side quests:
- Ancient Knowledge (+25% Armor if wearing all Dwarven armor, smithing skill increases 15% faster) received for completing Unfathomable Depths
- Sailor’s Repose (10% more health from healing spells) for completing What Lies Beneath
- Sinderion’s Serendipity (25% chance of creating an extra potion during alchemy) for completing A Return to Your Roots in Blackreach
These are received while completing quests for each of the "guilds" or organizations in the world:
- Assassin's Aegis (+25% Armor if wearing all Dark Brotherhood Armor) for completing the Dark Brotherhood quest, Sanctuary
- Dragon Infusion (25% less melee damage from Dragons) for completing the Blades quest, Dragon Research
- Prowler’s Profit (chance of finding additional gems in chests) for completing the Thieves' Guild quest, No Stone Unturned
- Nightingale’s Aegis (+25% armor if wearing all Nightingale set pieces) for completing the Thieves' Guild quest, Trinity Restored
Permanent blessings of the Divine
While all the Divines have temporary blessings you can get for visiting their shrines, Dibella and Mara have quests that allow you to get a permanent blessing from them:
- Agent of Mara (+15% Resist Magic) received for completing The Book of Love
- Agent of Dibella (+10% melee damage to the opposite sex) received for completing The Heart of Dibella
After completing the initial Greybeards quests that are part of the main storyline, you can speak to Paarthurnax who will give you one of three meditations:
- The Fire Within: the Fire Breath shout does 25% more damage
- Force Without Effort: You stagger 25% less while enemies stagger 25% more
- Eternal Spirit: +25% health regeneration while ethereal
You can only have one meditation active at any given time, but you can switch at any time by speaking to Paarthurnax again.
Nightingale Agent status
You can select one of three gifts after completing "Darkness Returns":
- Shadowcloak of Nocturnal: For 120 seconds you automatically become invisible while sneaking.
- Nightingale Subterfuge: People and creatures in the spell's area of effect will attack anyone nearby for 30 seconds.
- Nightingale Strife: Instantly absorbs 100 points of Health from the target.
These are permanent, activated powers that can only be used once per day. Similarly, you can swap between the three gifts by revisiting the Twilight Sepulcher, but only once per day.
These abilities are mentioned in the official strategy guide, but do not appear to be implemented in the game (yet?):
- Archmage's Authority (Better prices from members of the College) for completing the final College of Winterhold quest, The Eye of Magnus
- Gift of the Gab (speech skill increases 15% faster) for completing the Bards College quest, Tending the Flames