The Zune concentrates on being a Portable Media Player. Not a web browser. Not a game machine. Maybe in the future it'll do even better in those areas, but for now it's a fantastic way to organize and listen to your music and videos, and is without peer in that regard. The iPod's strengths are its web browsing and apps. If those sound more compelling, perhaps it is your best choice.
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.