These are 4e-ish changes I've implemented in 3e so far. Note I don't think I'll be moving on to 4e but some of the ideas make for mechanical improvements.
*Added IH style skill groups back when, replaced them with SWSE style skills when that came out and was clearly useful.
*Bo9S-once it tested out in play I melded the Bo9S classes into various PHB classes. Warblade into Fighter, Crusader into Paladin, Swordsage into Monk. Not made the Bo9S classes the new fighter, paladin, or monk. I added their powers into the existing classes altering as needed.
*Spells-adopted the recharge magic version post UA, then tried a hybrid of Bo9S and recharge. Currently using a completely homebrewed fast-recharging system. Search Token Casting System to find it.
*Saves-I've been reversing the saves and rolling against a static value since before 3.5e. It was just so much faster it couldn't be passed over when I saw it in the 3e DMG sidebar.
*BAB-currently experimenting with a 4e inspired attack bonus system. Divided into Attack Bonus, Grapple, and Magic Attack Bonus. I don't make the melee/ranged distinction of 4e. So far is similar to 4e in that is 1/2HD base +3 bonus.
*POL-this is NOT NEW. I've been doing this ever since 1e like quite a few DMs here, 4e just gave it a fancy name and lots of press.