I don't know if my rules qualify as house rules, because they don't change any written mechanics, but rather negate tacit assumptions. They're
listed on my House Rules page, though... anyway:
1) Teleportation is not quiet.
Dimension door causes an audible "bamph" (Listen DC 5),
teleport causes a thunderous boom (Listen DC -5), and
plane shift results in an earth-shattering kaboom (Listen DC -15).
2) Teleportation is not always instant.
Dimension door works as assumed in the books -- it is instant.
Teleport takes 3 rounds to transport you, and the "lost time" is spent somewhere outside the Prime.
Plane shift eats a full minute somewhere, but cross-planar events are wonky enough to not usually notice.
3) Pre-arrival is not silent.
Teleport starts causing a loud buzzing at its point of destination on the round when it's cast (Listen DC 5), which grows louder the second round (Listen DC 0), until finally the traveler appears in the aforementioned boom.
4) Off-topic but related: likewise,
levitate and
fly do not negate Move Silently. Each makes a humming buzz that is exactly as loud as normal footsteps. By concentrating, one trained in stealth can muffle the sounds.
Basically, it seems to me that it's not a problem with the mechanics, but rather with the assumptions that underlie the effects. (Unless you count the above as mechanics changes, in which case I think it is a problem with the mechanics!

)
-- N