Hi Stevev,
I have 5 ESX 4.1 server with vCEnter 4.1 and i want to migrate to ESXi 5.1. I have approximatively 100 virtual machines.
For the Esx 4.1 server, i will probably reinstall from scratch one by one.
There are a couple of things you can do:
1. First plan and upgrade the Virtual Center (on the new physical machine) and post that, you can think of either reinstalling ESXi 4.1 to 5.1 from scratch or you can use the Update Manager functionality to seamlessly upgrade the hosts from 4.x to 5.1
2. For the Virtual Center install, there are again two ways of doing this - one with your performance data and Inventory data, permissions, DVS configurations etc intact (saving the database) and the other way is just to install VC 5.1 from scratch and connect all hosts back to a fresh VC with no data carried over
For the fresh install, you can follow this link which pretty much talks you through all the pre-requisites
http://www.derekseaman.com/2012/09/vmware-vcenter-51-installation-part-1.html
Or if you want your VC 4.1 data to be intact:
1. Export the DB to the new VC and import the DB (VC) on the new machine
2. Follow the steps below
VMware vSphere 5.1 vCenter Upgrade Part 1. Single Sign On Installation - YouTube
For upgrading the hosts, you can check this
Install or Upgrade to VMware ESXi 5.1 Overview - ESXi - VMware Learning
Here are other ways to think of to see what best suits your need