I have a pile of house rules I've been working on, but I haven't sprung them on my PCs yet.
Very like Blue(23)'s background skills, I'm going to have each PC take an "Occupation", which will give them small boosts to related skills and allow them to do anything directly related to that occupation that's not covered by other skills as if by a trained int/wis/cha (depending on profession) skill check.
For example, a PC might take Sailor, getting +1 each to athletics and nature (for climbing ropes, navigating the sea, predicting weather, etc) and gains the ability to control any seacraft with a trained wis-based check.
Other things:
*trying to make unarmed strikes remotely worthwhile as a character build (
http://www.enworld.org/showthread.php?t=230320)
*add rules for disarm/sunder/grapple/trip/called shots
*change (slow it down) natural healing slightly so PCs ever have reason to ever avail themselves of a healer/doctor in town but don't need to go back to town for healing/rest for a day every hour of adventuring
*add encumbrance rules by volume in addition to weight, so the fact that a PC can carry 60 javelins doesn't mean they magically all fit in his belt pouch; it means his arms are full and they're in his way unless he finds a bag of holding, tenser's floating disk, or cart to dump them in.
*I really really want to redo the "magic item economy" extensively, in such a way that it is remotely capable of resembling a functioning, stable economy. I've yet to find any ideas how to do this yet though.
If you want more information on any of what I've made so far, ask and I'll post it here (or elsewhere if you prefer)