Looking back at my Eldritch Wizardry, Chainmail and Blackmoor books and comparing them to my Basic book and my AD&D books, I can see some pretty massive changes...some of them much more significant than some of the changes from 2Ed to 3.x.
They're all D&D though.
I've played about 100+ different RPG systems since I first picked up the dice- about 50% of them FRPGs, and I've come to the conclusion that there is a definite feel to D&D that seperates it from other FRPGs- not better, not worse- just different and distinctive.
Vancian magic and even some items. The accretion of game-specific critters, cultures, and archetypal NPCs.
There simply isn't a Vecna in Fantasy HERO, Talsiantha, or GURPS. Most FRPGs use a magic system more akin to D20 psionics than magic. Don't get me wrong- those games have their own legends, their own merits...
But they aren't D&D.