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SolarWinds Serv-U - SolarWinds Serv-U is a web-based, secure file transfer solution.
Beyond Compare - Beyond Compare allows you to compare files and folders.
CompleteFTP by EnterpriseDT - CompleteFTP is a secure FTPS and SFTP server for Windows.
WinMerge - WinMerge is an open source differencing and merging tool for Windows.
Progress WS_FTP - Progress WS_FTP is a robust FTP server solution that enables you to keep an eye on transfer details and security, accelerate file transfers, and protect your data with advanced settings and controls.
Meld - What is Meld? Meld is a visual diff and merge tool targeted at developers.