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Using Public Keys for Authentication
This article explains public key authentication in general. You may want to see guide to setting up public key authentication instead.
Do not confuse your user key pair used for authentication with host public key verification. Learn about all SSH key types.
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Generating Keys
To generate a key pair, use the PuTTYgen application.
Private Keys
Different file formats are used to store SSH-1 and SSH-2 private keys. While there is only one commonly used format for SSH-1 keys, there are several formats used for SSH-2 keys. WinSCP supports PuTTY format, as authors of PuTTY claim that it is the best one.
WinSCP also recognizes (but does not accept) the other two formats (OpenSSH and ssh.com), so it can suggest you to convert them. To convert the key file use PuTTYgen application.