Don't think there are many "secret" enchantments. I can think of Fiery Soul Trap, which is Soul Trap + 10 points of fire damage. You get that from a weapon in Ironbind Barrow. You can disenchant the Notched Pickaxe for a unique enchantment that buffs your smithing and does frost damage.
I think you can get another Magic Resist enchantment from the Shield of Solitude, letting you put two different Magic Resist enchantments on the same item, granted you have the Extra Effect perk.
That's it, I think. There are tons of unique artifacts with fancy special enchantments, but you can't disenchant them.
Sometimes I edit my sig so it continues whatever I was posting about.