Overall, I'd say Gen 3 has the best , though Gen 5 comes really close to beating Gen 3.
Gen 3 is home to my favorite Pokemon, Treecko, and it also has many cool designs and strong Pokemon. Absol, Tropius, Wailord, Solrock, Shiftry, Aggron, Kyogre, Electrike; just a few examples of my favorites from gen 3.
For Gen 5, I'm really falling in love with this generation. The games were amazing and it really shows how much the series has improved. Alot of Gen V Pokemon have become my favorite and are really strong. Such as Braviary, Scrafty, Krookodile, Hydreigon, Darmanitan, Reuniclus, Chandelure, Haxorus, Carracosta, Golurk, and lots more.