Most people don't use them. I personally think they can make the game much more fun. Below are the House Rules we currently use, how they work, and why we use them.
1.) 75-Card
All decks must have 75 cards in them, no more, no less.
Siply put, this allows for a bit more strategy and funner decks to make.
2.) Blind Evolution
Any Pokemon with a trainer, Dark, or anything else in it's name can evolve into any Pokemon they could normally evolve into and vie-versa (Ex. Misty's Psyduck can evolve into a standard Golduck, Psyduck can evolve into Misty's Golduck.)
Simply put, we don't have a lot of Gym set cards or Dark Pokemon, not enough to make a competitive deck out of anyways.
3.) NO Weakness/Resistance
All Weaknesses and Resistances are considered to be non-existant.
This is simply because we KNOW what cards are in each other's decks, practically by heart, and someone could easily just make a deck and sidelong everyone. The main reason for this is to decrease constantly dealing x2 damage and to just play.
Well, that's it. Please post your thoughts on the Guestbook and I'll tell you if we come up with or get rid of any other House Rules