I have always divided the rules in to two types. There are play rules and setting rules.
Play rules are things like to attack you roll a d20 add your attack bonus and compare that to the opponents AC to see if you hit. These rules I do not feel should be changed much. Changing these rules, while it can be positive, has three negative effects I am not willing to deal with. The first is that new players have a hard time joining the group and getting up to speed. Secondly, if you are teaching someone to play the game and you are using house rules they are likely to become very confused when they keep finding things in the book and you keep saying we do not use that here. The player can even feel that the game is stacked against them if this happens too much. The last disadvantage is that the more house rules I have the more crap I have to carry to the game. That being said I do have a couple house rules that I use, but I can count them on one hand.
Setting rules are things like races, classes, prestige classes, and the magic system. When it comes to these rules I feel it should be change at will. Changing these things are what gives a world its own unique flavor. Changing these rules does not really have any of the detriments mentioned for changing the play rules either. Firstly if you look at the PHB all of these areas have their own chapters and you can simply state instead of chapters x, y, and z in the players handbook we are using this document or this sourcebook here.
When I homebrew I change the races and classes a lot. I also make it so that a character cannot have a prestige class unless the training is offered in game. However, I leave those base rules alone. I learned my lesson when I tried to run a grim and gritty campaign, it lasted less then one session before we returned to the standard battle rules.