I believe most gamers house rule. Occasionally on the WotC/ENWorld forums, I'd run into hard-as-nails, rules-as-written types, but I think for the most part we all fudge, tinker with, and tweak systems as the experience of actual play dictates.
I was thinking in particular of an old Rolemaster campaign I was in (on the player side of things). The GM and one other player had been playing a long time, and had created extensive house rules for that edition of RM. However, he went along the lines of "if something is different, I'll tell you when it comes up in play". While this might work for a tweak here or there, he had changed a lot--and I mean a lot--of rules. Therefore, the players ended up feeling like things were too arbitrary, inconsistent, and confusing in a lot of situations. In hindsight, it was a campaign that underscored to me the importance of ensuring everyone is on the same page when it comes to rules. You don't NEED a house rule document--sometimes, changes are miniscule enough that a quick word at the start of a campaign is enough--but you do need communication about house rules.
So how formal are you house rules? Are they written down, just generally understood, or compiled into a pdf document?
Here's an excerpt from our (Castles & Crusades house rules, which are both handed out and kept on our group website (currently under renovation):
-The Game Master (or Castle Keeper, as it may be) makes rulings. We are not slaves to the rules.
-Attributes: If after attribute rolls your sum total of attribute modifiers is -1 or less, you may opt to re-roll until you surpass that mark.
-Challenges: The base challenge rating for Primary/Secondary stats has been changed from 12/18 to 12/15, which seems to work a bit better.
-Critical Hits: We will be using Arms Law to resolve critical hits. If you roll a critical, there is no need to reroll to confirm. You automatically do double (or triple) damage, as dictated by the weapon. However, you must roll a d6; on a 1-2, you roll an "A" critical; on a 3, a "B"; on a 4, a "C", on a 5, a "D", on a 6, an "E". You then roll percentiles to determine the additonal critical hit made.
-d30 Rule: Once per game session, a player may choose to roll a d30 instead of any normal dice roll. This cannot be used for any purpose during character creation or for hit point rolls.
-Initiative: Your Dexterity modifier is added to your initiative roll.
-Magic: Rolling a 1 on a casting roll equals a botch/critical failure, and can mean anything from a simple spell failure to losing the spell or opening up an unintended tear in space-time. Rolling a 20 is a critical success, and generally means the effect time, duration, or damage is doubled.
-Mass Combat: There is the very likely chance this game will see multiple instances of mass combat. Where appropriate, we will be using the Mass Combat rules from Farland World: http://www.farlandworld.com/battle.html
-Miniatures: Any placing of inappropriate miniatures, such as Giant Frogs or Golems on the table either in a) random fashion, b) an attempt to once again play out the "this represents my character" shtick, or c) an attempt to drive me mad, will result in negative roll modifiers for the entire night's play to be levied against the entire group.
-Mulligan Stones will again be used. They may be used to re-roll any player dice roll. Every character will start the game with one. They are handed out (sparingly) for good roleplaying, teamwork, great one-liners, fervent game participation, and general awesomeness. In a new twist, they may be used to add +5 to any one player roll (limit one Mulligan Stone per player roll).
A player may use their Mulligan Stone on another player's roll, provided that other player agrees.
-Powers & Feats: Feats or a 3.5-style skill system are not included in the game by default; however, bonuses and special statuses may be handed out by the GM/CK depending on circumstance, accomplishment, and how often you compliment me.
-Suggestions are always welcome! If something isn't working, let's discuss it. This is a game that lends itself to houseruling. Let's keep it simple, keep it fun, and make it ours.