This has been asked recently...I coulda swore there was a thread about this very topic within the last 3 weeks! Let an admin lock one up I don't care, tho.
And my answer is the same: you really can't say any one of them is the best.
GT1 has real make-or-break qualifying sessions. The attention to detail for the various series is mapped out more thoroughly (you can only enter a British or Japanese car in the British vs. Japanese series, for instance). However, since GT1 was the 1st game, PD / Sony only had licensing from a very limited number of carmakers outside of Japan, so you're pretty much stuck with the Camaro, Viper, Corvette, TVR (skip Aston Martin unless you like heavy piggy cars) and a slew of Japanese models.
GT2 has obviously tons more cars. For pure variety's sake, this one is my favorite but I wouldn't say it's the best. It also has the wheel shop, the JGTC series cars, the Event Generator (my favorite), and other features not found in GT1. However; the graphics are the worst of all the GT series. Some of the cars look decent whereas others look like shiny blobs! The game itself has an unfinished feel to it...the garage bug, car merging, sound cutouts during long races, bogus horsepower rating system, cars that don't sound like they should, the deletion of the turbo boost gauge and gearing charts from GT1...the list goes on and on.
GT3 has awesome graphics (duh) and I'm currently exploring this game. It's got crowd noise, tire noise (not just when you run up in the sand, either), the drafting dynamics are better, the littlest tuning tweaks to your suspension make obvious changes in handling, it even has those pylons you can knock over. But it lacks and lacks so many cars found in the first 2 games. Even the lowly Prelude is gone! It seems for every new thing Polyphony adds to each series, it'll take out or ruin another. But the race series makes sense again (you can only enter a limited number of cars in the Roadster series, for instance), qualifying is back...sort of (not nearly as demanding as GT1's). But for me the lack of so many models already has me curious about GT4. And of course by the time I get Gt4, GT5 will be out...
Yeah, none is really the best. What a silly concept.