Let's begin with Alistair. I actually think his mother is Fiona (from Dragon Age: The Calling). Some reasons why: 1) She slept with Maric, and he was Alistair's father 2) She had a child who had human ears and was a boy 3) Duncan cared very much for Alistair. He was Fiona's friend after all... 4) Alistair looks like Calian, it was mentioned in the Calling 5) Alistair is younger than Calian 6)"I can have him raised away from the court," Maric said, considering. "But people are bound to wonder who his mother is. Loghain will want to know. The child will almost certainly want to know... What will we tell him?" "Tell him nothing. Let him think his mother human, and dead." (From Dragon Age: The Calling by David Gaider) 7) Duncan also offered to take care of the child and bring news from time to time
And now I think Rhys' father is Greagoir, only because Wynne slept with a Templar, and he seemed to respect her a lot.
Please put comments on what you think :) Thanks