I have mine organized into a couple of basic sections. My "top" row looks something like

Albums
Jeff Radio
Angel Radio
Mood
Desert Island

Under "Albums" I have Genre->Artist->Album->Song in track order

Under "Jeff Radio"* I have "Rock", "Pop", "Christian" and "Worship" playlists, which are basically weighted so my favorite songs are emphasized in the given genre.

"Angel Radio" is my wife's favorites organized into "Country" & "Fast Country"

Under "Mood" I have "Instrumental", "Relax", and "Album Shuffle", the last of which really isn't a "mood" but it goes there anyway for lack of anywhere else. If played with the shuffle mode turned of it shuffles all of my decent, non-greatest hits albums and plays all of the tracks in order.

Finally “Desert Island” is an ever-changing list of my favorite ten albums so I have easy access to them.

Occasionally I’ll put newly uploaded tracks into a separate playlist at the root level called “new songs” too. I know there’s a shuffle mode for this, but I never get quite what I want that way. Gradually I let songs trickle out of this playlist as I get tired of them, and then eventually I just delete it.

Sorry if that's too much information, but this is what I've settled on after a year and a half of playing with this thing. I think the biggest controversy around here is whether to include a level for "genre". I couldn't image trying to click through all of my albums if I didn't have them separated, but to each his (or her) own.

*BTW “Radio” is used as my own personal joke to say that the empeg is basically the perfect “radio station”. All songs I like, no DJs, and now with cross fading!