Running the VM's created on ESXi 3.5 is supported on ESXi 5.x. After moving the VM's to ESXi 5.1 Make sure to upgrade VMware tools and Virtual Hardware version. If you are using VMware Standalone conveter for moving the VM's it will take care of upgrading virtual hardware during conversion process
If you are planning to perform copy of VM foldeter to datastore check Veeam FastSCP to perform the copy as it would faster