I've played all of the modern ones starting with Rorona, although I've yet to finish Nelke (it was a bit too difficult for me so I've kind of had it on hold). I did start Mana Khemia, but it was, uh, the PSP version, so that didn't work out; I might get around to it eventually.

My favorite soundtracks are probably Ayesha and Firis, and I think of all of the Atelier games they're the ones that have had the strongest influence on my own music. Both of them have incredible atmosphere and strong composition, and I love the different moods they convey. That said, I think Rorona should also get special mention because it's a standout in terms of cohesive composition and structure for the whole game, and I tend to go back to it when I try to think about fundamentals.