/head spinning/

For music and video I use the playlist(s) option. Create a playlist, or multiple playlists, drag the content you want into those playlists and sync to them.

Unfortunately there's no playlist concept for apps so if you have multiple iphones/ipod touches connected to the same library you just have to tick/untick the apps you want. But using the playlist concept for music is easy.

I agree with you and others that iTunes is pretty awful in comparison to most Apple software (it's not up there with iPhoto but that's a whole other post ).

iTunes has grown and changed over the years needing to adapt from just music to handling contacts, photo sync, apps, video etc. It doesn't have a single purpose like the rest of the core Apple apps and as such is a bit jumbled.

I think you'll find that once you get organised with playlists you'll be fine.