I'd say Gen 3 for the mainline games, since I quite like the 2D art and feel that the 3D background elements of the Sinnoh and especially Unova games tend to not look as consistent. (Gen 4 does have my favorite in-battle artstyle, though.)
Overall, I'd say: Gen 3 > Gen 4 > Gen 2 > Gen 6 > Gen 5 > Gen 1. (Haven't played 7/8/9 yet.)
However, if you count spinoff games, I'd go with Gen 4. The Ranger trilogy* has my absolute favorite artstyle across the whole series, and the Mystery Dungeon Explorers games are very very good as well. In addition, Battle Revolution did an excellent job with its 3D graphics, even though I'm not as much of a fan of 3D art as sprite art.
*I know the first Ranger was technically Gen 3, but it was a DS game and its non-Japanese release dates were after the Japanese release dates for Diamond and Pearl, so I kinda think of it as an honorary Gen 4 game.