Vampire:The Masquerade

Clans -
Rule: There is no Assamite Clan. Instead, Assamites are a secret society. Quietus is a Discipline that is taught to those loyal to this society.
Reason: First of all, I always thought the very idea of a clan whose sole purpose is to destroy all other clans is pretty silly. It promotes shallow, cartoonish villains, and flies in the face of Vampire's otherwise cloak-and-dagger style storytelling. Secondly, Assamites are essentially Vampire Ninja, and that type of antagonist works best when you don't see them coming and can't figure out who is who. As a secret society, you never know who the Assamite is - they could be that Nosferatu you just met or that old Toreador friend of yours. And you never know what other Clan Disciplines are going to be combined with Quietus. Thirdly, it prevents me from having to put up with whiny players who want to start off the game playing an Assamite. I can just say "a what?"

Disciplines -
Rule: Dominate 1 does not require a 1-word command; you can use a full sentence to issue the command. However, the command must be a simple action that could be completed within 1 combat round, and the command goes into effect immediately. Therefore, a command like "Sleep" would be ineffectual because most people can't simply decide to fall asleep at the drop of the hat. Similarly, saying "go away" might cause the target to turn around and walk away for 1 turn (6 seconds), but then the effect would wear off. You still cannot order a person to do anything that would cause direct harm to themselves.
Reason: I simply find the single word command very limiting. Allowing a simple sentence makes the power work more like what you see in classic vampire movies, which I think is always more fun. Since you still need Dominate 2 to give complex commands, or to give commands that won't kick into effect until some time in the future, I don't think this changes the scope of the power all that much.

Rule: Each dot of Fortitude provides +1 Bruised Health Box, in addition to the +1 die to soak.
Reason: While being able to soak Aggravated Damage is handy, I've always felt that Fortitude should be an effective counter to Potence, and it simply wasn't. Potence grants automatic damage, and Fortitude only grants a 50% chance of reducing damage. In addition, Fortitude took a big blow when 3rd edition allowed for characters to roll extra damage based on how well they hit someone. Suddenly, an extra die or two to resist damage is not so impressive. Combat is so infrequent in my games (which is as it should be), and Fortitude is such a defensive ability that it very rarely comes up. In fact, it's rare that my players ever pick up more than 2 dots in it, preferring instead to go with something that they can use more often. This houserule is basically an incentive to make the Discipline a more attractive option to players, and also to give it a serious boost in combat. The extra Health Boxes can make a big difference early in a fight, but they tend to get used up fairly quickly, so in most cases it's perfectly balanced.

Rule: When playing Dark Ages with Cappadocians, the Mortis Discipline has been completely reworked.
Reason: This rule actually has its own article on the house rule section of my web site. Go there for more info.

Humanity -
Rule: Instead of having characters role Humanity to determine how many combat rounds they can stay awake when their daytime slumber is disturbed, players can safely assume that their characters can stay awake for a number of minutes equal to their Humanity score. In addition, a character does not need to make a perception check to wake up if he takes at least 1 Health Box of damage.
Reason: Let's be honest here - if a Vampire is trying to wake up during the day, 9 times out of 10, it's becuase they believe they're in some sort of danger. Making a character roll perception to notice that they're burning in the sunlight or allowing a character only 2 combat rounds to defend himself against vampire hunters sounds a bit too much like instant-kill. Players don't like to be sucker-punched like that, and Game Masters really shouldn't be so heavy handed. Allowing a couple minutes of action allows a character a reasonable amount of time to defend himself in combat or move deeper into the shadows while still preventing them from doing too much during the day.

Rule: I have created my own hierarchy of sins table, which you can find elsewhere on this site.
Reason: I don't mind the sins that White Wolf presented, but I personally think their table is a bit too simplistic. I've seen too many times when players and game masters disagreed on what sort of actions should cause a virtue check, and which are justified. Personally, I just think my table is easier to follow.

Rule: Your Humanity score does not determine how long you stay in torpor after losing all your health boxes. A vampire who is given a blood point immediately uses it to heal 1 point of damage, effectivly bringing the character back up to "Incapacitated". Any additional blood they are given can then be used as normal. Of course, a vampire in torpor who is only given 1 blood point to revive is almost guaranteed to be in a state of frenzy at the slightest provocation, but it's better than being in a slumber for a year.
Reason: The recovery chart presented in the main rule book is harsh. A character with a Humanity of 5 needs to sleep for a year before they can wake up. Even a vampire with a relatively normal Humanity of 7 is out of the game for 2 weeks. While thematically this makes sense, no player wants to be left out of the game for that length of time.

Rule: Your Humanity score determines how quickly you wake up each night.
Reason:Since the house rule above effectivly removes some of the bite (no pun intended) from letting your Humanity drop, I needed some other means to subtly reward players who maintain a higher rating. Therefore, in my games, characters with a higher Humanity rating wake up before characters with a lower rating. I don't use any chart or table to determine how much time passes - I pretty much play it by ear. As a general rule of thumb, someone with a Humanity of 8 or 9 will have an extra hour or so each evening when compared to someone with a Humanity of 4 or 5.

Ghouls -
Rule: Ghouls cannot spend blood to heal or to raise attributes. In fact, don't bother keeping track of how much blood a Ghoul has at all - they either are a ghoul or they're not. Instead, ghouls heal at a naturally accelerated rate (1 non-aggravated Health Box per day of rest), and their Kindred master can feed them blood to heal faster (excess blood fed to a ghoul is immediately spent to heal wounds, but it's not something the ghoul can "bank" for later use).
Reason: The game is called "Vampire", not "Vampire & Ghouls". While a ghoul should be significantly more powerful than a mere human, they should NEVER be able to pose a big challenge a vampire. Otherwise, what's the point of becoming a vampire in the first place?

General vampire "biology" -
Rule: There is nothing to stop a vampire from having and enjoying sex. They may not have the same biological drive as humans, and the act may not be enjoyable for the same reasons, but that doesn't mean they can't perform or derive some sort of pleasure. It does, however, cost a blood point to engage in such activity.
Reason: Come on, seriously? Look at how many movies out there pair vampires and sex. It's been incorporated into the myth that vampires are alluring and seductive. I really don't understand White Wolf's insistance that vampires are never interested in doing the deed when there are so many other reasons besides the basic biological drive that causes us all to think about sex. A vampire may perform sex as a means of gaining someone's trust, as a way to reward certain behavior, out of boredom, becuase they're curious, for the simple joy of making someone else happy, as a means to exert control over someone's emotions, or any number of reasons. A fair warning, however - if you do chose to engage in such pass-times, it's very likely that your partner will realize you're not breathing, do not have a pulse, and are cold to the touch. When you're lying naked next to someone, it's really hard to fake that.