Found a lore deed for gathering lore entries and a deed earned because of how I handled the villagers in Rill when doing quests and I've got one for earning Anjali's trust.
Also, the deed I got for solving the password problem with the talking door was Solver of Cipers, +2 agility. I also gained one at the end of the Gunderic quest.
You also gain at least 1 deed for completing side-quests. So far, those are the ones that don't pertain to the main story (deeds that you theoretically miss). With story deeds included, I've got 7 deeds total.
So far, I'm level 13 and haven't played more yet since gaining Katarina, my second companion. Current game time is 5 hours and 57 minutes.
I think you can actually NOT do the Gunderic Mansion if you want. So the deeds in there are actually also Non-Story Deeds.