My favorites...
Gen IV: It was the most advanced the sprite work seemed to ever get, as Gen V's really didn't seem any more detailed or well developed. I love most of the Pokemon sprites, the world is beautiful, and it just has a nice feel. When it comes to 2D graphics, this is my preference.
Gen VI: The graphics I prefer universally. If I had a choice, I'd completely forget about the 2D graphics and have all the games be 3D. It gives the world so much more life. The Pokemon have so much more personality, the animations look so much better, and it makes things like trainer customization possible. Nothing at all against 2D graphics... but this just worked so well for me.
As for the worst...
Gen III: I just really, really dislike the GBA's graphics in general. There's something about the weird plush colors and blurry textures that doesn't sit well with me. It's probably a big part of why I couldn't get into Emerald or even Leaf Green very much. I hated the look of them. Now, had I played these games when they were NEW? I'd have probably loved them, because they were the biggest graphical advancement in the series next to the dimensional jump.
Gen V: It's basically Gen IV's... except it had awkward 3D models mixed into the overworld and really... REEEEALLY ugly moving sprites that were just excessively pixelated and awful to look at. I appreciated the innovation and ambition, but it just ended up looking so... bad. I did like some aspects to it, like it showing the scale of some of the areas, but... I just don't miss it in the slightest.