There are some runes you have to complete tasks for, and those tasks aren't necessarily pointed out to you. For example, after a certain mission you speak to Callista and she tells you to find Emily. Once you find Emily, she gives you a rune she found washed up. I was wondering, as I want as many runes as I can, what other runes are secret like this?

I think there's another if you non-lethally deal with Lady Boyle.

When returning to the Hounds Pit, always pull out the Heart and check to see if anything's around. You can get several runes and a bone charm there, but have to time it right or they disappear. The bone charm, for instance, you can only get if you talk to Cecelia at the right time.

Aside from the mentioned one, I can only recall the one Trevor gives you after returning from "Lady Boyle's Last Party", if you dueled Lord Shaw and came out victorious.

I think you get this if you keep the other two Boyle ladys alive and (not 100%) don't ruin the party.

This is true. On my last game, I killed the target and snuck out and still got the rune.

The letter thanks you for keeping 'most of her family alive' as well.

You get two by doing granny rags missions, however the second mission forces you to poison slackjaw and yhe bottlestreet gang im pretty sure

I think he meant not directly quest related.

List: (Generic starters, not giving the answers to finishing)
-Talk to Calysto all the time - she will be sitting at a table in the Houndpits Pub and will tell you to go find Emily, go do so.
-Slackjaw asks for the safe combo. Go use the safe combo first.
-Trevor Pendleton gives you one when you return from killing Lord Shaw? (is this quest GIVEN, I don't remember)

As far as I remember, I think he gives you the letter and tells you to deliver it, but doesn't give details. The duel caught me by surprise the first time through.

and if you don't dual lord shaw he gets in a huge snit over it. but he doesn't tell you about the contents of the letter and it's sealed so corvo can't read it prior.

Emily finds one washed up on the Beach at the Hounds Pit, can't remember between what missions it happened though. Her and Callista are playing Hide and Seek, with Callista having given up and just sitting in the Hound's Pit. Ask, find Emily, plus one Rune.