For the longest time, I defended the AD&D organization of spells by class and level as being the best way to do things. It made more sense, I argued, when selecting a character's spells for the day.
However, at the urging of some folks here a few months ago, I decided to undertake an experiment with the Adventures Dark and Deep book. There, I simply included everything, cantrips included, alphabetically. The spell lists are still there, of course, organized by class and level. But the spell descriptions themselves are alphabetical.
I've been using my pre-prototype copy for personal use over the last couple of months, and I've got to say that the new system of organization is a huge improvement, at least in my experience. Having the spell lists makes daily spell selection just as easy. I'm experimenting with the same sort of scheme for magical items in the GMT, and it looks like it'll be equally useful.