×I did NOT
-Save the Jarl/ask him to free Kraka,
-Turn the "doom" Squirrel into the "bloom" Squirrel,
-Choose the humble response when introducing myself.

Actions I am certain were Honorable;
1. Didn’t steal the boots. (City, upper level)
2. Gave Angrimm the golden apple (In the keep east of the lake)
3. Did not tell Angrimm a false tale
4. Gave Sigurd the mead of poetry
5. Asked Kraka to stop thieving,
6. Reunited the lovers (destroyed Fremont's shield to do so)
7. Accepted / won Skrymir's challenge,
8. Saved Alviss, and did not mock him.
9. Buried Guard in front of the troll cave in chapter 3
10. After bringing the skull of Sigrun’s husband to her, I put the skull back, closed the casket, locked the crypt, and returned the key to Sigrun.
11. Ignored money pouch in the tomb.
12. Picked no lock, didn't sneek around / steal

Things that MIGHT have affected my score;
1.Displayed Andvari's armor, as per his request, but only in taverns, and not EVERY person.
2.Gave Gem to Snorri, but did not chose the “I’ll never speak to you again” option.
3.Fought/killed Fafnir in battle.
4.Bribed Snorri to release Kraka
5. Did not steal the tinderbox in the Keep. (found it on a bandit’s corpse)

×Fafnir

×taking the gem from the holt
telling a false tale about guybrush threepwood

×I think taking the gem isn't stealing, as it's unclaimed in the middle of nowhere. I was able to get 98% honor even after taking the gem, so the chances of it counting against you is pretty small.
At first I thought that telling Arngrim a false story might lower your honor (According to how Skrymir describes honor) but as Radiant Explained above, boasting and "talking big" isn't considered dishonest in Viking society. I’m still uncertain though, so you may want to refrain just to be safe..