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I have to say, that I was skeptical at first and I tried your FTP server and its great. Great job with that. The config screen for SSL access is especially nice... great job making it easy to understand. ;-)
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.
Edit:
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.