Use kubuntu it's much nicer to transition to coming from windows.
The default media player can sync to ipods, just not apps (you can do that on the touch anyway). for a better experience I recommend banshee media player which is just amazing.
I dont know about the windows phone however but I'm 100% sure if someone has found the code to make the sync possible theres a linux alternative
What about all the playlists i have in itunes? Will I be able to keep all of them.