We just deployed Gene6 FTP Server onto our shared platform. It performs pretty well (1200-1300 sites per server), it's not expensive, and it has a COM API so you can script pretty much all of the configuration without too much fuss.
When OP originally asked this question 'A free version is a must' was not specified at the time I answered.
The two biggies are Filezilla (free) and Serv-U. I've had really good luck with both of them. Serv-U has gotten progressively more expensive over the years. I seem to remember it being really cheap at some point.