The Companion set introduced D&D's first prestige classes, and the 3rd edition skills system owes a lot more to the Cyclopedia's skill system than to AD&D's NWP. Additionally, dragons were more similar to the Companion Set's advanced dragons than to AD&D dragons with their "hit points per age category." D&D 3e also followed the basic rules in collapsing the longsword and broadsword into one weapon, not including a khopesh, and so forth.
3e monks, like RC's Mystics, have acrobatics and extra attacks per round.
The 3e combat grid is more like Basic D&D's, with the exception of using 5 foot squares and making reach a general rule.
"Max hit points at first level" is an optional rule from Basic D&D.
So many systems were similar it would be hard to trace on to the other.
Some AD&Disms that made it into 3e: the Outer Planes and the Astral Plane, larger hit dice, bonus spells for high ability scores, cover, XP costs for spells, two axis alignment, Druid wildshape, paladin base class, thief-acrobats (in 3e, most thieves are thief-acrobats), Underdark races, the elven sub-races, gnomes, separate race/class, etc.