Linked Clones using the official vSphere APIs is a functionality of vCenter and not something that is exposed in ESX or ESXi, the script that Duncan has mentioned requires the use of vCenter + licensed copy of ESX(i). However, Linked Clones in essence is nothing more than just some fancy pointers from your Linked Clones VMDK back to the parent VMDK. Here are two scripts that I wrote before VMware officially released an API that supported Linked Clones with the release of vSphere, prior to that, you would have needed to use Lab Manager to get this functionality and now products like View & core vSphere platform supports it natively using VMware's APIs.
Linked Clones on ESX - http://communities.vmware.com/docs/DOC-9020
Linked Clones on ESXi - http://communities.vmware.com/docs/DOC-9202
I will caveat that I've not touched these scripts in awhile and they've been tested when vSphere 4.0 was initially released, but I've not tested this officially against vSphere 4.1, you may or may not run into issues. Though in how the scripts work, I think you should be fine but definitely do test this in a lab environment.
Will try out the scripts in ESXi 4.1 and update accordingly, hopefully it will be smooth.
Now I have vCenter Server 4.1 standard installed in my datacenter and 3 ESXi 4.1 hosts added to vCenter Server, my ESXi hosts are installed with vSphere 4.1 Enterprise Plus licenses. I would like to know how can I configure linked clones using the vCenter Server?
Any ideas will be highly appreciated.