I was making a list of our House Rules but most of them were gotten from somewhere else, and while trying to credit their sources I found that almost all we use comes from HBO.
We use pretty much everything from there: Inventing Spells from Lab Texts allowing different TeFo combinations, Minor Seasonal Activities, Die Roll Conventions (on stress rolls 1 is botch chance and 0 is roll again and add 10), Botching and High Skill (except we lower botchs by -1 for ability scores from 6 to 8, by -2 from 9 to 11, by -3 from 12 to 14 and so on), The Truth About Faeries, Demons "Without Virtue", The Price of Lab Texts, The Roots of the Arts (though we usually change the roots in Muto and Imaginem for Intellego and Herbam), Cantations and Correspondence XP, Exposure XP, Fast-Casting, Specialties changing and fractional Vis. The only thing of there we usually leave out is Creatures with Might being able to get Exposure XPs without their Might getting in the way: if anyone wants to train his familiar, he needs to feed it a lot of vis (except now that I just read that rule of letting 3 x Silver Cord easing the learning penalty I think I'm going to suggest using it).
We also use some other things from other people. We got from ironboundtome the possibility of trading magnitudes for +3 bonus in finesse rolls in spells, and pregnancy, birth, children & gift inheritance rules from here.
Next, penetration issues: on my current saga we have agreed that enchantments cast to an item do not have penetration issues if they just affect the item, getting rid of pink dots. So a sword with an Edge of the Razord do penetrate Parma. Everyone agreed after one player argued that it was silly that he the forceless casting of that spell over rival weapons would put every grog and companion in the party in more danger but would make him immune to these weapons. It also helps designing enchanted items, that now can have active effects without bothering to add penetration modifiers as long as these effects affect only the item when they are active. We now have cool swords that can glow in the dark because people actually desing these effects not fearing to ruin the weapon's penetration just because it's glowing. Our main trouble there was that then invisible weapons should bypass Parma as well. We agreed to that adding at least 2 extra botch dice (it's dangerous to wave around something sharp that you cannot see), but it have definetively caused an increase in the frequency of magic creatures with second sight we found and the danger of enchantments, which is cool.
Next, XPs an seasons stuff. As we usually start sagas with spring covenants, we allow the setting of basic labs with a 0 penalty in just one season, instead of requiring 2. I've have also have more than enough new players impatient to play their magi and wanting to do stuff with them being suggested to spent half a year of their young lives setting a lab. We also houseruled that some lab improvements like installing minor virtues can be done as the same time as the lab is being used considering it a distraction: opening a window, drawing a circle or a installing a mirror doesn't seem to us like the kind of work that requires 3 months, even if you have to do a lot of mystical work around them. We also extended correspondence rules from Covenants to any character who can write correspondence (and does so). And then we extended them even more. Two characters argued that they could write to each other and we also allowed that to happen more easily: we call it dinner-table-talk-xps and they must come from the 4 XPs pool of correspondence: it's a nice way to put magi together at the dinner table and it can give some funny results (we had two magi discussing penetration for a whole year and getting some xps each in the ability for the insights of their debate, while two other magi got their xps in guile because they were making jokes on them and yet another magus getting these xps in carouse because bored of all that stuff he used to get drunk listening to his fellows).
And then there is combat. We allow two weapons combat, even when I use it more for flashing rival NPCs than player characters. As shields are listed in the Weapons table and combat modifiers of using a Long Sword and a Shield are exactly the sum of the bonus of the two, our party proposed that the usage of 2 weapons should be allowed just by adding their modifiers. But the Init +4, Atk +8, Dfn +2, Dam +12 that would result by using 2 long swords would make a Round Shield an useless prop and a Great Sword a weaker weapon (if true medieval people carried around a shield they must have had a good reason to do so), so we changed the Shield Defense bonus to 1 + 2 x [Previous Value] and ruled that any two single weapons could be used together by selecting a primary weapon and a secondary weapon (and each round he may decide which is which) and halving the stats of the second weapon, rounding down, requiring only that the Str required to handle both weapons is the sum of the two weapons' values plus 2, one per weapon and 2 extra botch dice. So in our current saga a swordsman can use a long sword and a round shield (and needs a Str of 1+ to do so, 0 from the sword, -1 for the shield, +2 for two weapons) in two ways: focusing on attak, and then he would have the usual modifiers of Init +2, Atk +4, Dfn +3 (being +1 for the sword, and +2 = (1 + 2 * 2) / 2 rounded down for the round shield), Dam +6, or focusing on parrying, having Init +1, Atk +2, Dfn +5 (being +5 because of the shield and +1/2 = 0 because of the sword being now the secondary weapon) and Dam +3. And our fancy swordmaster companion can swing 2 Long Swords with a combined Init +3, Atk +6, Def +1 and Dam +9, without making our Point Grog feel stupid of his Great Sword stats of Init +2, Atk +5, Def +2 and Dam +9 wich just trades a point in initiative and another in Atk for a point in Def and the safety of two less botch dice than the fancy companion. And anyone with only a single weapon can now swing a Dagger to add +1 to their manage, but they don't usually do so because, well, two extra botch dice can be quite scary after you have seen a couple of combat botches.
And some character creation rules: we added Code of Hermes 1, Order of Hermes Lore 1 and Profession: Scribe 1 to the magi required starting abilities. We force every character to pick at least one Area Lore of the place were they grew up unless concepts forgives it, for example by having been raised by diabolist and spending all your childhood inside an empty barrel, though I'd vote to make that character still purchase Area Lore (Barrel)... Grogs are encouraged to be designed not as meat grinders, but trying to add some color to them making them pick one odd, useful for stories virtue, varied abilities (like Music, or Proffession: Cards player, or Area Lore: Barrel...), and not getting -3 in Com and Pre by default to boost their combat characteristics.
Finally we have our take on House Diedne, that I guess it's more an expansion that a house rule at this point: their V&F's go in a Ex-Misc way, what allows them to get Diedne Magic (and Dark Secret) for free and leave empty the Major Hermetic Virtue to get also Life-Linked Spontaneous Magic, and to be hidding into some other house, mainly Merita and thus get Faerie Magic as their free minor house virtue, and we have some of their inner mysteries and paths designed, the jewel of the crown being the path that initiates them into Chthonic Magic. A Diedne magus with Diedne Magic + Life-Linked Spontaneous Magic + Chthonic Magic is a fearsome beast either to play, avoiding being suspicous, or as an NPC, being hunted down or marched.