Depends on what kind of FTP you are looking for.
If you need ftp which is easy to set up and don´t have much experience with linux use Serve-U or Bulletproof FTP (use to be G6FTP).
If you wan´t to run a warez Site with extensive usermanagement and scripts running (sfv checker, dupe checker .....) get raiden ftp.
If you want to go for linux and only need a anonymous site or an simple ftp for your users i would recommend Proftpd.
But the best ftp of all is definatly
glftpd. It has all the features a windows ftp can give you. There are scripst for everything you can imagine. The rights management ist totally independent from the linux userrights.
It takes some time to initially configure the server but the documentation is really good. (but if you can´t handle configuring with text editors in config files stick to a windows ftp).
The whole usermanagement can be done with site commandos.
Works with most ftp clients that can handle raw commands. There are also some windows and linux tools to configure the users over site commands. (Gui which configures the ftp over a normal ftp connection). It is rockstable (had an uptime of over 208 Days).