So what are your houserules?
This requires some thought...I have thought of many to use, but only implemented a few of them, which follow here.
(1) I've come to grant PCs a free rank in a single profession skill, to represent "non-adventuring knowledge". One of them had Profession (miner)...see #7 below
(2) I tend to explain the use of Strength checks vs. damaging doors/walls/etc. until destruction as an attempt to beat through the obstacle in a single blow, vs. just nickel-and-dime'ing it to death.
(3) To break ties with initiative rolls, I let the character with the higher Dexterity score go first. If those are tied, then the higher Wisdom goes first. Failing that, Intelligence. I don't use total initiative modifier at all.
(4) I worked out my own stats for Craft skill check DC and Craft field for almost all items in the main PF books. In several cases I had to get a little creative and create a few new Craft fields, and in certain situations the item required a Knowledge: Nature or Knowledge:Engineering check in addition to (or instead of) a regular Craft check, such as for astrolabes and magnets. I really hope the upcoming Ultimate Equipment book will be incorporating information like this. (The Paizo people are welcome to have everything I wrote or they can write their own, either is OK with me.)
(5) To start one campaign, I had the PCs play as 0-level minions of an evil wizard who was about to get run out of town. The players created all the stats for the classes they would become, but the PCs did not have access to class features other than weapon proficiencies, spells, skills, and starting equipment. They also had only 1 HP (plus Con Mod too, I think). There was a lot of action going on and most of it was projectiles. I was generous, and only a couple of the PCs were actually hit, and they kept each other alive with Heal checks.
(6) PCs invariably have to loot the bodies of monsters they defeat. I did not want the party rogue (being the Perception specialist) to be able to end up with all the good stuff while everyone else got short-changed, so I implemented the following system:
* Looting bodies is considered part of a combat encounter, which is to say that even if all enemies are dead, the PCs still take turns as per usual.
* Looting a body is considered a full-round action that provokes an attack of opportunity. It consists of taking a move action to come adjacent to the body (if necessary) followed by a Perception skill check (results forthcoming)
* For any monster or enemy NPC of significance, I pre-generate a treasure table either during private prep time or if necessary during combat or immediately prior to the first looting attempt. (Though not intended for it, this system can work for random encounters if you have pre-gen tables for every type of creature on your "random encounter" table which would normally be found with treasure.)
* I make a concealed roll on the treasure table pre-made for the creature. Each looting attempt allows only one item to be retrieved (which can be a single weapon in its sheath, a single scroll in its case, a small container holding two healing potions in it, or perhaps a small bag of various gems--each can be considered one "item"). For convenience I use a table equal to the size of a polyhedron (so 4, 6, 8, 10, 12, or 20 items, depending on the amount of treasure carried) and would only use a distributed percentile table if I really needed to. Each item will have its own Perc skill DC, which is usually between 10 and 15, but can be higher for particular small, well-hidden, or camouflaged items. If your Perception roll doesn't beat the DC, it means you didn't find anything that moment, or you couldn't get your hands on it, or maybe you didn't recognize the significance of what you were looking at. Remember also that deceased persons rarely collapse into a pose that is convenient for looting, so time must be spent undoing buttons, rolling bodies over, wiping blood and gore off objects, etc.
* As items are eliminated from the treasure table, the blank spaces remain. If you get a blank space, then no matter what your Perc roll is, you won't find anything. For example, the rogue acquired item #5 on the list and then the fighter also got item #5, he could roll a natural 20 on his Perception but will find nothing. Moreover, because the treasure table is concealed, some items can be very well concealed, and I allow repetitions to take place, it is impossible for the players to be 100% certain they have found everything of value that can be discovered. They might be willing to spend the time to strip the corpse naked and thoroughly search everything, or they might not have the time or patience for that. At any rate, this system stops one PC from monopolizing all salvaged equipment as a tool of manipulation against the rest of the team.
(7) I allowed a PC to create alchemical Acid from scratch using Knowledge/nature and Profession/miner, using materials scratched off the walls of a mine.
(8) I allowed Survival applying Int modifier to read a map of a dungeon in order to figure out the most efficient path from their present location in it to a section they wanted to visit. The map was fairly old and obsolete, so the DC was 20 or 25 for every attempt to navigate the dungeon by map alone.
(9) This is technically not a house rule but is a useful practice anyway. Whenever I generate a NPC or a monster whose encumbrance I might need to keep track of, I scratch out the light, medium, and heavy load values on the standard character sheet and instead write down "Medium Load", "Heavy Load", and "Max Load". For each I write in the minimum in pounds for each of these. My reasoning is that every creature is under a light load by default, and ideally wants to stay in that range. For this reason, and for simplicity's sake, I see only the need to track of the minimum values (rather than the ranges as given on PSRD's Table for Carrying Capacity) for each load category.
(10) In determining random encounters during an extended travel period, I make up a table of monsters that would fit the environment, and then I figure out a Fifty-Percent table, which is the estimated amount of time that would pass, given the environment and the party's general attempts at stealth, for the odds of a random encounter to reach 50%. The 50% table has different time ratings for different Party behaviors, such as: camped near the road with lit fire, hiding in the bush keeping quiet, etc. I ask the players what their characters will be doing for the time being and then, based on my 50% table, fast forward to the next time interval and make a percentile roll against 50%; a roll of 49 or less results in a random encounter. For example, the PCs are traveling through light forest staying on the path, making a forced march with little noise. I determine these circumstances would add up to a 50% encounter chance at every half-hour interval, so I advance the "campaign clock" a half hour, roll percentile dice, and get a 73, so there's no encounter. Fast forward another 30 minutes, roll for encounter, and so on. The players can always decide to be more stealthy (or less) with their PCs from one interval to the next, but only after I have rolled for a random encounter for the current time interval.
(11) I used something like the following mass combat rules for a large number of combatants:
* All monsters of identical race, HD, and class levels (if any) are combined together into a formation, similar to the rules for a mob or swarm.
* Formations are considered to possess its members' individual attacks, equipment, and special abilities, as well as covering the entire space occupied by its members. Thus a formation with archers, heavy shieldmen, and polearm-wielders have all the attacks given, and in general each such attack originates from the most convenient square occupied. A single opponent adjacent to the formation's front line (assuming it occupies a tight square) can expect to receive three attacks at most from the shieldmen of such a formation, but could receive many more attacks from the formation's polearm-users due to reach, and potentially all the ranged attacks from the formation's bowmen.
* Formations add up all members' HP together into a single HP pool rather than having each members' HP total tracked individually. Every interval of damage taken equal to a member's full HP (whether from the same damage source or different sources) removes one member from the formation. The specific member to be removed can be chosen semi-randomly (from the front line if from a melee attack or from the center if a ballistic attack, etc). For instance, a formation of 100 standard goblins with 600 HP total will lose 1 goblin (and one attack) for every 6 points of damage the formation takes.
* Formations being targeted with area attacks make a separate save for each member targeted. Before rolling any dice, I calculate the minimum number needed to succeed on the save, and then if there are 20 or fewer formation members being targeted then I roll separately for each one. If more than 20, I assume an equal number of members will have rolled for each value from 1 to 20. In the case of the formation of 100 goblins, I will assume five rolled a natural 1, five rolled a 2, five rolled a 3, and so on, and then work out how many failed, and then remove according to damage taken or place effect markers accordingly. Of course, this creates an unintended consequence of "the few dying for the many," where all the damage gets effectively concentrated on as few members as possible--especially when an area damage effect should not have killed any one member at full HP, bear in mind we are having to work on a higher level of abstraction when a large number of creatures are in play, and it's impractical to track whole companies and battalions of creatures fighting each other while also keeping the pace of combat flowing at a rate tolerable for the players.
(12) In some campaigns, I have allowed PCs to simply have max points every level instead of having to roll for them.
(13) In almost all my campaigns, I have used the following system for ability generation: Roll 4d6 drop lowest seven times and then take the six scores you like the best. This has kept players from getting stuck with a negative-modifier to an ability who didn't really want one (and those players who might like the RP opportunity presented by one get an extra chance at having one.)
(14) Probably since mid-last decade I have exclusively used group XP. Which is to say, all PCs earn XP at the same rate. If anyone does something to earn XP, even if its on a side-quest or an activity exclusive to their class, everyone else in the party gets to benefit too. This avoids problems such as:
"So-and-so's PC is a level or two behind everyone else because the GM never gives them any situations to be useful in."
"So-and-so's PC is a level or two ahead of everyone else because they are always hogging the GM's attention."
"So-and-so's PC is a level or two ahead of everyone else because the player is such a class clown or a stupidly awesome character actor, the GM is always giving him bonus XP for his goofiness or natural talent."
Even when I give out bonus XP for good roleplaying or good solutions to problems, _everyone_ benefits, not just the person who earned it for the group.
When it's time to give out XP, I usually ask the players the following after I've given out the normal XP awards for defeating enemies and achieving story goals:
* Did you do anything else that you think you should earn XP for? (and I deal with everyone's answers in turn)
* Did /anyone else/ do anything that you think deserves XP? (this is aimed at rewarding players who might be too timid or humble to boast, and for cases where a person didn't think they did anything exceptional, but everyone else thought it was awesome.)
* Is there anything else you players think you should get XP for? (I usually don't go this far unless they are really getting close to leveling up, and I am just looking for an excuse to put them over the top.)
The following house rules have never come up in play, but given the opportunity, I would use them.
* I allow all of Paizo's classes in my games (and treat Anti-paladin on equal standing with Paladin) and would be willing to allow levels in Anti-Paladin for a PC who is ostensibly ex-evil, even an anti-hero, if I feel I can trust the player to roleplay a character who would not totally nuke the broad storyline that I've been sketching out, or cause in-game strife between PCs that would lead to out-of-game conflict between players.
* I'm also picky about which classes from 3PP I would allow, based on their flavor and the perceived niche they would fill. But I would allow Artificer, Priest, Warlock, Warlord (Adamant), Armiger, and Shaman (Super Genius).
* Lastly, it's never come into play, but I stick to a level limit of 60 for NPCs...I hold to a metaphysical "level barrier" at 20th and 40th levels. To get past 20th level, a character has to accomplish a great quest worthy of an epic level character. To get past 40th level, the character has to achieve immortality (easier with divine consent/promotion, harder without) and thus join their world's pantheon. Within each campaign world's pantheon there are only so many "slots" available for levels beyond 40th level for demigods (immortals without worshippers or the ability to grant spells) and deities. For instance, there can be only one 60th level character, three 59th level characters, and so on, which culminates in a limit of 400 immortals for any given world.
* Related to the above, within my cosmology there are 144,000 worlds (coexistent material planes, each its own campaign setting), within which new worlds are constantly being created and older ones falling under judgment either to pass into glory within the constellation of the upper planes, or cast out into the lower planes in eternal damnation. Within each new world, the mortal races are mostly left to their own devices to figure out how to ascend to immortality, all the time under the perpetual supervision of celestial servants and being vulnerable to the machinations of dark minions. Every world spends a thousand or more generations in the great river being contested by the forces of good and evil, until the end of times when that world has reached its 400-immortal limit. Then the cosmological wheels are set in motion for that world's final judgment and discovery of its ultimate fate--purification and destruction of evil for all time, or else the rapture of the faithful and the rescue of what little virtue remains, before the rest is cast into the great abyss, never to know anything good or decent anymore.