I had access to the fastest supercomputer at the time (a T3E with 64 nodes) as well as a small linux cluster.
The speedups I saw on the super computer were: 60X for 64 nodes. The speedups I saw on my linux cluster were: 4X for 8 nodes. All the problems were due to the slow network (10Mbit ethernet with TCP) and congestion (allreduce hammers the network). However, I didn't have to wait a week for my job to start running, and I could add more nodes and run different jobs in parallel.
I concluded that, unless I had an MD jhob that couldn't fit in the linux cluster, it was always better to use the linux cluster instead of the supercomputer.
It really depends a lot on the simulation and how much you can adjust your system to run faster on smaller machines.