Kanto: Celadon City. No matter how many times I go there I love it. You can fight Erika, and buy stones, and use those stones on an Eevee you also get from there, the game corner, fatally maiming and injuring Rockets, and the cute Poliwhirl OW sprite. I always had a lot to look forward to here, and the name just sounds nice to me~
Johto: Although I am tempted to say Fuscia because that's where the last tine I ever saved on my Silver Version was despite it being Kanto, I will instead go with Olivevine and Mt. Silver. Olivevine had the nice sidequest of helping a sick Pokemon by traveling to another town and back, as well a rival meeting, I always forget to go here and head off to Mahogany so when I come back my team is nicely overtrained, etc etc..... I believe I heard Brendan/May came from here as well? I always assumed Goldenrod was their town cause of Ruby from Pokespe
Hoenn: Route 117 was where all of my post game energy went. I trained against the double battlers and triatheletes almost daily, I hatched eggs there, and I encoubtered my first shiny there(Wingull~). Mauville was right next to it and that was where I hubted Latias at for a good long time until I caught her at Mt. pyre instead. In OrAs I loved the PlayerxRival date in Mossdeep though. ;D
Sinnoh: Although I have not yet finished my Diamond Version I got last October, right now my favorite area is Snowpoint Cuty and the Lakes. I love the cold weather and snow, so Snowpoint is so perfect. If my team wasn't already full I'd have caught a Sneasel there too..... The Lakes hold obvious meaning to the game, and I enjoyed that part of the story.
Unova: Maybe it's just the nostalgia of the first towns, but Nuvema and Aspertia are very nice to me. And the Nimbasa Musical is where I spent many pre-E4 and PostGame hours with Minccino~ Not to mention battling alongside my little bros at the Battle Subway. XD
Kalos: For once, the Victory Road stuck out to me. Rather than a feeling of 'Get through this' it felt as though it held special meaning. Countless trainers have walked down here before, and now you are. The music upped this very much, and I go back for training lots. The final battle is OK though....