House rules are fine but there should be an explanation as to why they exist; in my experience if there isn't a compelling, well thought-out one - for instance sometimes the only reason has been 'that's how TR used to do it' - then they shouldn't be there in the first place.
Look at it this way, what are the reasons we use published mechanics? It's mostly because they're already known by many players so they're already experienced at them and they've been developed by professionals, right? Well, if we have too many HRs then those factors are invalidated - and I'm not saying that's necessarily a bad thing, only that there needs to be a good enough reason for it.
The other small peeve I have about HRs is they're sometimes not all in a single place but they're scattered over different helpfiles or wiki pages. For example I was going to buy Claws of the Unholy for my Gangrel on Reno when I was told it didn't exist. It's little inconveniences like that.