In my mind, halo CE wins, by far.
For one, in multiplayer, the sheer fact that you can choose what you want to play, and who you want to play with makes the difference. I agree, halo 2 had a system with a combination of halo 3 and halo CE, but there where way more hackers that made it no fun, and, correct me if im wrong, but i believe halo 1 was the only one that was totally free online. Also, with halo Custome edition, you can get maps from every halo game and more (pluss make maps and weapons!!! how cool is that!) I haven't really tried reach much, so im not really sure about that.
Halo CE was the only one that had cool mods, and was easy to hack (adding a whole new layer to the game) The goal of hacking was to make the game more fun, rather than make yourself win (opposite from other games)
As for innovation, halo ce started it all.
Music... meh, i don't listen to music at all, so who am i to judge this
The story; they where all good, though i only really paid attention to read and halo CE
Oh, and dedicated servers in halo ce where awsome (moded snipers, tank brawls, etc.)
So, all in all, halo ce wins, although i have only played reach and halo 2 a couple times. The only thing i enjoyed about halo 3 was slayer and random weapons.