I'll go against the grain and say I don't agree with Diablo. Diablo defined the genre, but per the OP, others have surpassed it. Sure they may be "clones" (another testament to what Diablo achieved), but they still advanced the genre.
IMHO, Darkstone, Titan Quest, all 3 Divinity games, even Torchlight can contend for the crown. I'm not going to claim which one is "best", but I do think Diablo has been surpassed technologically, mechanically, etc.
I tend to think this way for most of the genres. Doom was genre defining as well, but it didn't even have proper mouse support out of the box. For the FPS, I would claim Half Life 1 is still king (but I would claim its contested by many other great games). IMHO, Painkiller made some great strides in weaponry, secrets, buffs, replayability, use of lighting, alternate playstyles, etc. If you don't pay attention its a standard shooter, but if you acknowledge all of its subtleties, its one of the better ones.
The only genre I feel is truly uncontested is the FPS (sneaker) where Thief still reigns (opinion, of course). The only contender was Splinter Cell and it forced combat in too many places for me to appreciate it as an advancement of the category. Chaos Theory came very close, but it lacked the setting, atmosphere, lore, charm, etc.
If we can account FPRPG as a genre then I would have a tough time picking between 2. Deus Ex and Bloodlines, but I would likely give the nod to DX1.
I haven't played enough in the RTS genre to make a solid claim, but every game I've touched after AoE2 has seemed inferior (or at best, the same).