I'll tick 'em off by generation:
Gen I: Champion Blue Theme by a mile. Both the original the the remixed FR/LG versions are amazing, the B/W version isn't quite as good but still very cool. The Gym Leader theme gets an honorary mention also, and earns second place for the Gen I music.
Gen II: I'm not going to count Ho-Oh's theme here since it was HG/SS that had that and not the originals. That said, this generation had the best music in my opinion - Dark Cave, the Olivine Lighthouse/Mt. Silver theme (ESPECIALLY Mt. Silver since you were heading to face Red,) the Trainer Battle theme stands out as being pure awesome in 8-bit, and the Rival Battle theme also gets an honorary mention here. Shame that none of these tracks were done justice at all with the HG/SS remixes, but the GB Sounds item rectifies this issue nicely (thank Arceus...)
Gen III: Not much of the music stands out for me here - the Regi theme was OK, Ky00ber/Groudon/Rayquaza was pretty cool, and the Elite Four/Champion themes rocked for R/S/E, but other than that, I didn't find the music in R/S/E as memorable as any of the older or newer generations. Hoenn being an awesome-looking region makes up for it, but hey, that's a whole other topic so Gen III ends right there.
Gen IV: Sinnoh was...meh for music overall except for a few very stand-out themes: Cynthia Battle, Dialga/Palkia Battle, Frontier Brain theme, Distortion World theme and Giratina (Platinum) theme. HG/SS had the awesome Ho-Oh theme and a bunch of butchered remixes. Next...
Gen V: Team Plasma Battle theme wins. Plasma Boss N Battle theme also wins as well as Geechisu's battle theme. Other mentions go to the odd but interesting "Low HP" theme that plays along with the bleeping alarm of past generations, and the crazy-as-hell roaming legendary theme that sounds extremely weird yet extremely cool at the same time.