I am assuming itunes only but I don't have an iphone but I do have an ipod and you can only do stuff on the ipod through itunes im assuming its the same way.
I'm assuming when you say "iTunes" you're referring to stuff from the iTunes music store. Because, you have to use iTunes to sync your iPod. But, you can rip CDs into iTunes. If your music is already on your hard-drive, just import the music into iTunes. Supports any non-DRM-ed formats, for the most part, including non DRM WMA files.