Diamond & Pearl definitely, though Black & White comes close. I just love both Gen IV and V games and a manga chapter based on their story are just awesome. First time ever I truly fell in love with all the new main characters introduced, previously there was always at least one character I didn't care that much about (Red, Gold, Ruby). My favourite characters (Green, Silver, Crystal, Sapphire) tend always to be overshadowed by other main characters, in DP chapter they were equally visible. Also the biggest reason is that Diamond, Pearl and Platinum journeyed as a group for the most part of the chapter. Previously it was mostly every character on their own, sometimes meeting and then dashing of, which makes the chapters blurry.
Other good chapters include Yellow, HeartGold & SoulSilver, Platinum and Emerald.