So many good ones in this thread. But seeing as I spend most of my time as a DM, I'd have to say the 4E monster rules are on the top of my list, as of now.
The multiclassing in 3e was an incredibly cool idea to me. Yeah, there were problems, and, yes, I didn't use it that much. But the fundamental idea was golden.
My favorite addition were feats. I loved them as ways to give a focus or theme to your character and loved how they let you have two of the same class that could play very different.
AD&D -> 3.x: Death of THAC0. At one point I had a computer that did all the table lookups for me (TRS-80) which really sped things up, but still... ick.
3.5 -> 4E: Monster stat blocks being decoupled from player rules... because I no longer need to lug along a monster manual AND a players handbook to understand how a monster works... all the rules in one stat block is elegant.
One of my favorites was the change to the magic creation rules in 3e. It was far from perfect, but I loved the fact that creating a magic item was no longer just something for NPCs or that PCs did after they reached name level, bought a tower and retired from adventuring.