The one program I sometimes use with my iPods is MediaMonkey. By the name it sounds silly, but in general it's a decent program that works for our family's iPods, my Sony Walkmans, and my Creative Zen X-Fi. It's available as freeware, though I was so taken by it that I actually upgraded to the paid version (it unlocks a number of features that I felt I needed, but it's not necessary to upgrade if you don't want to).
The old standby Winamp also works fairly well and reliably with iPods. There are others as well, but with my limited (or non-existent) use of these I couldn't go as far to recommend any of them. But the following link is a list of many of them on Wikipedia:
I should note that I still use iTunes a LOT to manage our household's various iPods. I use it on a fairly old computer still running Windows XP that serves as my media storage machine. I've finally come across a build version that doesn't crash or lock up the DVD drive; I only wish that the stupid program would stop nagging me to upgrade every so often, but for now I can live with it.
As for the current Zune: no, it's NOT compatible with Windows Media Player. It uses its own proprietary software officially called 'Zune'...confusing the heck out of people who normally call the player 'Zune'. Most users just refer to the software as 'Zune Software', and leave it at that. I can't remember for sure, but I think that a copy on CD came with my Zune devices, though nowadays it wouldn't surprise me if you have to download it from zune.net, the official Zune website. Microsoft created this program because they wanted to copy Apple and its iTunes Music Store marketplace. WMP already served other devices and services, and Redmond didn't want its new music store being used by people who owned other makes of players...in theory stunting Zune sales, or music sales of their own music store for Zune owners looking to shop around for their tunes. Hence, a proprietary program for the Zune, and the Zune alone.
As I mentioned before, the Zune player does not work with any other management software other than the official Zune program (at least without hacking it), and it's THIS program that likes to break things for other software that I use for other players, most notably iTunes but I've had issues in MediaMonkey as well. The problems it creates are with the tag data that shows up on the screen and the album art; if you're ONLY using a Zune you'll never notice it. But if at some point you decide to change to another device like an iPod, you could have problems down the road. As I'm in a mixed-device house, owning a Zune does have its headaches (sigh).