Just a few house rules we use, thought I'd share:
1) The Aqualung can be used to spend a turn in flooded rooms. Just like the rules for being outside the sub, if by the end of your next turn you are still in a flooded room, you kick the bucket.
2) The Harpoon can be used in combat with the Crazed Gnomes variant, just like the crowbar. It gives a +1 bonus to your attack roll.
3) You can choose to low-flood a room connected to an exterior hatch if you are coming in from outside the sub.
4) When resolving Fire, if the roll lands on a room already on fire, treat it as a Fire Spreads card.
5) When resolving a Fire Spreads and there are no fires in play, treat it as a Fire card.