Welcome to the Community - First thing have you reviewed VMware's Upgrade Guide? - http://pubs.vmware.com/vsphere-51/topic/com.vmware.ICbase/PDF/vsphere-esxi-vcenter-server-511-upgrade-guide.pdf
There are two routes for you to move the VMs over to the new environment -
- You can use VMware's Standalone Converter and V2V to the new environment. This method will work and cause the least amount of reconfiguring and disruption to your environment
- Add the 3.x hosts to your new 5.1 environment - I would not look at vMotion/Storage vMotion as you will need to create a cluster with EVC to be able to vMotion between the hosts as the CPUs will not be compatible for vMotion but use cold migration - this will allow you copy the VMs changing both the host running the VM and move the VM to a new datastore.