Going from ESXi 3.5 to VMware Server 2.0 is a major downgrade. You should really be looking at upgrading your ESXi 3.5 to ESXi 4.1.
ESXi 4.1 will outperform VMware Server 2.0, in nearly every aspect.
But if you really want to migrate a VM from ESXi to VMware Server, here is what you should do:
Note: The virtual machine that you want to migrate should be powered on and running on the ESXi 3.5 server, and this VM should be contactable on the network by the VMware server machine and by the machine which will be running VMware Converter.
1. Download Converter Standalone 4.3 from http://downloads.vmware.com/d/info/datacenter_downloads/vmware_vcenter_converter_standalone/4_0
2. Install Converter 4.3 on a Windows machine which has access to both the ESX server and the VMware server machine.
3. Once Converter is installed, launch the application and select "Convert Machine"
4. Once the conversion wizard is displayed, select "Powered-On machine" as the source type and select "A remote machine".
5. Provide the IP details and the login credentials for the specific virtual machine that you want to migrate and click next.
6. In the destination selection screen, select "VMware Workstation or other VMware virtual machine" as the destination type and select "VMware Server 2.x" as the VMware product.
Note: You need to have some sort of network share available so that you can tell Converter where to store the virtual machine files.
7. Click next and proceed through the remaining screens in the conversion wizard.
8. The conversion should start and complete.
9. Go to your VMware Server 2.0 installation and login into the interface.
10. From within VMware Server 2.0 choose to open an existing virtual machine and browse to the location where you converted the virtual machine to and select the VMX file.
11. You should now see the VM listed in the VMware Server interface and you should be presented the option to power it on.
Hope that helps.
