The downside of Sharepod is that it no longer supports uploading of files onto the ipod and is no longer being properly developed. However for taking files off the ipod I prefer it, as it is simpler, loads faster and just seems less buggy.
Yamipod has more features and will let you upload files onto the ipod. It could function as a simple iTunes replacement, but I find it quite often just stops working without telling you why it had a problem, so I use it less than Sharepod. If I was using just one of the programs however Yamipod would have to be the one, because it is still being developed and improved.
I do use Mediamonkey sometimes because itunes is ridiculously slow with a large collection of music, but as an ipod manager it pretty much beats everything else out there if you use all the ipod features. So Mediamonkey will handle music but not videos, contacts, photos, nike support (for the nano) etc, and if you use all of that then iTunes really has to be your choice.
Mediamonkey will allow you to take files off the ipod but it doesnt do the renaming of them or placing them into appropriate folders that Yamipod, Copypod and others do. All OK if you don't mind files called KASZ.mp3 sitting around in no particular order, but otherwise you would still need another app to relabel them (mp3tag or other mp3 taggers would do this but not create folders, or perversely itunes itself would do both).