I recommend foobar2000 in combination with windows explorer. Foobar has a copy to function that can create a sensible folder structure based on your tags. This lets you manage the music on your player as a playlist within the application...which is pretty damn convenient. Create a playlist...right click, 'copy to', pick a destination and folder naming scheme, click copy. I use this to load music up on my rockbox player, and it works like a charm.... It really doesn't get any more raw and flexible than this for automated management, and I can always just hop into the folder structure in windows to delete stuff if I want....

Same thing with Media Monkey (which is what I use).

You can easily point it to the card in your phone and tell it to copy any of your songs there in any format you want (conversion from X to Y) and in any structure you want. It can include album art if you like (I did that and it shows up on the phone perfectly) and you can tell it to add effects including basic ones like leveling the audio which is good for phone use. All of that can be saved so that, in the future, you just select the phone as a device and keep it all in sync as desired.