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Do you know of a FTP service that have a good looking web interface so that clients can login in, download files and upload files. Preferably customizable so i can put my brand on it. And that uses a cloud service like Amazon S3.

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up vote 0 down vote accepted

While not FTP per se, YouSendIt has been around for a while, is reasonably priced and is fairly trivial to embed the upload form into your Website to allow files to be securely transferred to you.

Once a file has been uploaded, you receive an email notification with a password-protected download link.

Another option would be to roll your own with an Amazon EC2 instance running PHFTP backed by S3 storage.

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