MediaMonkey is a decent alternative to iTunes.
As for Foobar, I've never used it with my iPod, but it does have a menu for iPod, I guess it works the same with iPhone. Should be File > iPod/iPhone > Synchronize, Manage Content or whatever you want to do.
Edit: I just found out you need a plugin to use it with an iPod, not sure if it works with an iPhone, but take a look around the hydrogenaudio forums.