Hey I have had MP3s and other digital juke boxs other than Apple but the I Pod is still going to be the best overall.
Yes I Tunes can try to take over a non Mac system but what software dosent.   When loading any software check out how to load it first so that it affects the least amount of programs before you load it.
I do alot travel by air and this does keep you relaxed on those over packed flights and keeps the nut case in the seat next to you from trying to talk to you.
I Pod or MP3? I have had 2 to 3 of each and the next will be Apple.