When a person has children, they need to start planning for the future, and what they'll leave behind for their descendants once they're gone.
Various stories, including Ezio's 'relations' with his lady apprentices, and Leonardo's Box.
Assassin's Creed I/II, Prototype
The mildest of one-sided Ezio/Altair
When Desmond, Malik, Altair and Ezio all live under the same roof, shenanigans are bound to ensue... especially when Altair is turned into a tiny, adorable cat-boy.
Several short stories, ranging from pre-ACII, all the way to Brotherhood.