Every game table and DM have their own brand and style of play.  Every gamer I've met has used house rules on just about every game they play.  When finished I hope to have listed here the house rules that I've incorporated into my game.  These are presented in no particular order.

Don't Roll a One! - When a natural one is rolled on an attack, the attack is an automatic miss.  This is core rule.  I add to this the rule for the fumble.  When an attack roll is a natural one, it is a threat for a fumble, the player rolls again to confirm the fumble.  If the second roll is higher than a one, the attack is a miss, but not a fumble.  If the second roll results in another natural one it is declared a fumble and the DM consults his many interesting fumble charts to see what has gone awry (see DM log for examples of fumble charts).

Languages: At character creation, all races in Kinthur receive reading, writing and speaking their native language for free.  Their native language will depend on their upbringing. Half-elves and half-orcs can choose, based on their upbringing.  For each additional Intelligence modifier a character has, they get a language slot.  A single slot can be used to Speak or Read/Write a language.  So a human created with an intelligence of 12 (+1 modifier) would get Common for free, and have one slot to choose to Speak or Read/Write a second language.  Not all your slots are required to be filled at once.  They may be saved for a character to learn another language in the future, after sufficient exposure to it (DM's discretion).  Upon earning skill points at leveling a character can spend skill points to learn another language.  As standard practice, this is a cross class skill for everyone, but a single rank in a language allows you to speak/read/write the language.  Some have asked me about adding additional ranks.  As a house rule, I would allow a +2 synergy bonus to disguise if you have five or more ranks in a language when impersonating a creature of  a particular race.  For example, if a human rogue disguised himself as an orc and he had five ranks in speaking Orcish, he'd get a +2 synergy bonus to his disguise  roll.

Lightning Bolts Don't Bounce! ok, just to clarify.  the spell Lightning Bolt and similar effects do not bounce.  This includes spells that seem like lights and rays.  They don't bounce. 

Last Second Saves! This one is controversial.  If you receive damage that is your DOOM, placing you below -10 (also a house rule) then you are DEAD, however, I will give until the end of the round for you to die completely.  This means any allies you have that have not gone yet in that round, still have a chance to save you, IF they can do enough healing to bring you back from the brink of DEATH.
As for the -10, I do use the "hovering on Death's door" rules option, (3.5 PHB  p.145)

The Defense Roll (3.5 DMG p.25)  In a nutshell, I allow the defender of an attack to roll a D20 in place of the static 10 for Armor Class.  This allows more randomness, therefore, more fun for me. 

Automatic Hits/Misses/Critical/Instant Kills: ( 3.5 DMG p.25)   A natural 20 is an automatic hit, and threat for a critical.  A second roll is made, using the same bonuses.  If the second is successful, then the hit is a Critical.  If the second roll is a natural 20, then it is a threat for an instant Kill.  A creature immune to criticals is also immune to instant kills.  A natural 1 is an automatic miss, see above for rules regarding fumbles.