As Windows users, your choices for managing MP3 and other audio files are nearly limitless. Honestly, many of these applications are at least good or excellent, so which one(s) you choose should be based on other considerations. For example, if you're going to access your media collection from a Media Center PC or Extender in the den, you should organize your content with Windows Media Player (free with Windows, but make sure you've updated to the latest version), since those hardware products derive all of their song meta-data from that application. Zune guys, obviously, should use the Zune PC software. Those with iPods, iPhones, or even Apple TVs (all 6 of you--relax, I'm one too) will want to use iTunes. If your primary access point for music is another type of portable player, you'll want to use whatever software works with the device; typically, that's Windows Media Player, but it could be RealPlayer too. Either will work fine.
While there are some conceptual differences between these products--I use iTunes and Windows Media Player primarily at the moment, but plan to use the new Zune 2.0 software extensively when it ships next month--I don't believe many people will have issues moving back and forth.
Personally, I use iTunes to manage the "master" copy of my music collection. That is, I allow iTunes to organize my music collection into whatever folder structure it likes, which makes it easier to backup and copy from system to system. I use iTunes to create playlists, apply album art to my song files (the automated system Apple has works pretty well but I end up having to manually copy many album art images), and rate songs. Rating songs is actually really handy (if time-consuming) for creating smart playlists: For example, a greatest hits CD from a particular band is quite easy to make when you've rated all the songs. Apple's iTunes also works well for finding song duplicates. It has pleasing visual styles like the Cover Flow mode and has recently turned into a first class video player too. (We'll look at that in a different article.)
iTunes isn't perfect, and certainly there are some advantages to other players. Windows Media Player and the first generation Zune software both feature excellent "stacks" views of artists and genres, which are quite nice. And though you can't play DVD movies with iTunes, DVDs works just fine in Windows Media Player.
Frankly, there's no reason you can't use all three. Zune is the most agnostic and interoperable play of the bunch, and it quite nicely copies over the meta data you've already configured in iTunes and Windows Media Player, (It even picks up iTunes ratings, which is key.) Otherwise, you should look into MusicBridge, which was my software pick of the week in Episode 35 of the Windows Weekly podcast. This wonderful and free utility lets you manage your music collection in either iTunes or Windows Media Player and then manually (but very quickly) apply meta-data like album art and even ratings to the song library in the other app. This is genius and it really solves some of the real world issues that arise when moving between these applications.