Sounds like you'll need some form of LDAP on top of your standard filesystem. Same thing as MS Windows has, although Linux's options are free (MS's is added onto the version price tag), and sometimes overlooked when Linux is installed. Another option (although a pain in the neck), is to have a database manage the directories, but I'd personally opt for an LDAP of one flavor or another.
http://www.openldap.org/doc/admin24/
Alternatively, your distribution probably has a somewhat easier package that preconfigures a lot of the items mentioned in the link above.