I voted Gnomes.
If dwarves weren't so overpowered in 3.5, I'd have voted for them possibly, but I dunno. Elves (and half-elves) are a bit underpowered in 3E, and they're just over-used and cliched now as far as most people are concerned (myself not included), so I wouldn't expect them to be all that popular if they were the only non-humans on the block. Halflings would be tougher to stretch and mangle into different niches and cultures for a setting, by themselves. Half-orcs (and orcs) are too limited and underpowered in 3E.
Gnomes are more versatile than these others, and probably more balanced. Gnomes are fairly tough for being little people, so they don't necessarily suck as warriors. They're not drastically superior to humans in sneaking about (no Dex bonus, no sneaky skill bonuses except the +4 size bonus to Hide), with no bonus feat or extra skill points. They're talented with a bit of magic, and they're well-suited to alchemy and inventing stuff. Gnomes can be tricksters and range from villainous to fey-like to schitzophrenic to innocent jokers. They can be scary manipulators and trap-makers, or peaceful craftsmen and merchants. They're scholars of magic but also tenacious protectors of caves, hills, and forests.