I needed an FTP server to perform functional testing of some FTP client Java code (commons vfs). The top 5 Google results for "Java FTP Server" were:
Apache MINA FtpServer - Runs as standalone or embedded; free and open source (Apache License)
FtpGoServer - Runs as standalone; source can be purchased
jftpd - Runs as standalone; appears outdated (last release in 2001); incomplete implementation
Java Secure FTP Server - Runs as standalone; free and open source (GPL)
Colorado FTP - Runs as standalone; free and open source (LGPL)
My pick is Apache Mina FtpServer. It's an active project. It can be easily embedded into any functional test -- the alternatives require peering into the source, writing adapter classes, etc.. It's also the only one that shows significant activity in Google Trends.
UPDATE 5/26/09: Documentation of Apache Mina is pretty thin (as with the other FTP packages).