Samba can certainly do roaming profiles for Windows machines, and assuming Mac OS supports them, it should work as well. Samba can easily replace a Windows NT4 style domain controller, though the last time I worked with it, Active Directory support was not quite there yet. You didn't specify anything about the current network setup, so I don't know if that is going to be a problem for you.
I am not 100% clear on what you mean in that last bit, I guess you are trying to ask what the better hardware would be for $3500. Without a lot more information on your needs and the topography of your network (how many users are we talking about, how much space is each one allocated, etc, etc), it is pretty much impossible to make any sort of hardware recommendations.
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