Sorry for the huge review, but I'm really loving the new Zune, and hope this, as well as the excellent reviews some other people have written, will help you decide if it's the right choice for you.
Hands down, Apple's app store wins by a mile. It's a huge selection of all sorts of apps vs a rather sad selection of a handful for Zune. Microsoft has plans, especially in the realm of games, but I'm not sure I'd want to bet on the future if this aspect is important to you. The iPod is a much better choice in that case.
Sorry for the huge review, but I'm really loving the new Zune, and hope this, as well as the excellent reviews some other people have written, will help you decide if it's the right choice for you.