Bob's right, in that this is one of the primary functions of a domain server, but there is a sort of work around for it. It's really only workable for 2-3 users/systems, after which it will quickly become more work than it's worth.
You have to create a local user account for every user, of every machine, on each machine. Then go to each machine, and set individual permissions for each of those accounts on the shared directories. As you can plainly see, the effort required to maintain this will grow exponentially with every new user/system.
Another approach would be to create a new user group, and then apply all the permission settings to that group. Once you make the individual user accounts, if you make them a member of this group, the permissions for that group will automatically apply. This is still a lot of work however, so it's probably better to focus on an entirely different way of sharing files.
If you used FTP instead of SMB (Windows file sharing), it would be much easier to set directory permissions for every user. The biggest drawback, is FTP is a client-server system, and SMB is peer to peer. The way FTP would work best, is if you had a fourth system which served as a central repository for files. Otherwise, you have to run a FTP server on each system, and you don't gain a whole lot, effort wise, over SMB.
There are other distributed file systems like NFS and AFS to consider. As I recall, NFS offers no security, but is very quick and easy to set up. AFS offers quite a bit of security, but is not the easiest to get going on Windows.
You could also attempt to set up your own Linux and SAMBA based domain server, but unless you're very familiar with the Unix AND Windows way of networking, and think you would be able to mesh them together, I wouldn't attempt it.
The long and short of it is, Windows was never designed with networking in mind, and all the networking features were just sort of bolted on later. Hence the limitations you're running into.
Best thing I could recommend is a Network Area Storage (NAS) device. They cost anywhere from $50-100 at most electronics and office supply stores. They're simply little devices that let you connect and use external hard drives over your LAN. Much more energy efficient than a 5th computer doing the same thing.