How to manage linux workstations with policies
Solution 1:
You may have difficulty switching between Windows and Linux mindsets. You might want to take at configuration management engines, like bcfg2 and puppet.
Also, I'd recommed taking the time to read www.infrastructures.org, a brilliant description of large-scale Linux administration techniques. I'm certain some ideas there could apply for your situation.
Solution 2:
There's no product like Group Policy for all distros (e.g. fedora or ubuntu). What there is, are exclusive solutions (similar to Microsoft WSUS) for each distro: like Landscape for Ubuntu, or RHN for RedHat but these solutions are paid and are focused on updates, monitoring, patching servers.
You can apply restrictions or limits to Ubuntu (I belive fedora or other distro that use Gnome too) with solutions like Sabayon to define desktop profiles. But AFAIK, this solutions are not centralized.
Solution 3:
RedHat's Spacewalk is the free version of RedHat satellite (local implementation of RHN) which handles things like system provisioning and package management (from my limited understanding of MS technologies, I think it is similar to System Center Configuration Manager).
Spacewalk specifically states in the features that you can "manage and deploy configuration files" I wasn't able to find any details for how that works, but it might be something to look into. In any case, there is nothing out-of-the-box that would work like GPO, and like Neto mentioned, Spacewalk only works with Redhat-derivatives (Fedora and CentOS). There isn't anything that would be cross-distro.