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.
The new Zune browser is surprisingly good, but not as good as the iPod's. It works well, but isn't as fast as Safari, and has a clunkier interface. If you occasionally plan on using the web browser that's not an issue, but if you're planning to browse the web alot from your PMP then the iPod's larger screen and better browser may be important.
This is getting a bit more subjective, but I much prefer the Zune Marketplace. The interface is colorful, has more flair, and some cool features like 'Mixview' that let you quickly see related albums, songs, or other users related to what you're listening to. Clicking on one of those will center on that item, and another set of "neighbors" will come into view, allowing you to navigate around exploring by similar artists, songs, or users. Speaking of users, the Zune "Social" is also great fun, letting you find others with shared tastes and becoming friends with them. You then can listen to a playlist created based on an amalgamation of what all your friends are listening to, which is also enjoyable. Those concerned with privacy will be relieved to know you can prevent the public from seeing your personal listening habits if you so choose.