Aside from having the blessings of the gods and using the guardian stones,
How many permanent active effects are there?
Here are the only ones I know of:
Resistant to disease (Werewolf ability after completing the first couple companion quests) The Three Totems (offering three abilities) (Werewolf quest given by Aela) Ancient Knowledge (Unfathomable Depths quest) Sailor's Repose (Frostflow Abyss quest)
Are there any others? Seeing as how awesome ancient knowledge is, I would love to know what other permanent (or semi permanent like the blessings) active effects there are
If you do all the Mara related quests in Riften, you get the blessings of Mara, which is +15% Restoration iirc. --- The one plus of playing Skyrim on an SDTV? Unless you know what they're called beforehand, you read 'Draugr' as 'Derp'.
List can be found at: http://www.uesp.net/wiki/Skyrim:Abilities#Abilities
As well as those you mentioned, main ones are Agent of Mara (15% magic resistance, Book of Love quest), Sinderion's Serendipity (25% to create two potions at once, from crimson nirnroots quest), Prowler's Profit (higher chance for gems in chests, find all 24 unusual gems), some full armor set bonuses (nightingale, shrouded armor) and species abilities.
(Blades potion effect I believe is still glitched / not working, so exclude that. They can GTFO with what's needed to get it anyway).