I just bought a new Raspberry Pi 3 and was not able to connect via SSH, even after creating an empty /boot/ssh file. SSH client under linux showed the following:
$ ssh -v 192.168.0.32
OpenSSH_6.6.1, OpenSSL 1.0.1f 6 Jan 2014
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 19: Applying options for *
debug1: Connecting to 192.168.0.32 [192.168.0.32] port 22.
debug1: Connection established.
debug1: identity file /home/vlad/.ssh/id_rsa type -1
debug1: identity file /home/vlad/.ssh/id_rsa-cert type -1
debug1: identity file /home/vlad/.ssh/id_dsa type -1
debug1: identity file /home/vlad/.ssh/id_dsa-cert type -1
debug1: identity file /home/vlad/.ssh/id_ecdsa type -1
debug1: identity file /home/vlad/.ssh/id_ecdsa-cert type -1
debug1: identity file /home/vlad/.ssh/id_ed25519 type -1
debug1: identity file /home/vlad/.ssh/id_ed25519-cert type -1
debug1: Enabling compatibility mode for protocol 2.0
debug1: Local version string SSH-2.0-OpenSSH_6.6.1p1 Ubuntu-2ubuntu2.8
debug1: Remote protocol version 2.0, remote software version OpenSSH_6.7p1 Raspbian-5+deb8u3
debug1: match: OpenSSH_6.7p1 Raspbian-5+deb8u3 pat OpenSSH* compat 0x04000000
debug1: SSH2_MSG_KEXINIT sent
Connection closed by 192.168.0.32
SecureCRT at the same time complained about protocol version mismatch if SSH v1 was selected, and just indicated closed connection for SSH v2.
Apparently, the SSH keys (/etc/ssh/ssh*key) on the Raspberry were all of zero size for some reason. To fix that I had to run the following commands from the terminal:
$ sudo rm -r /etc/ssh/ssh*key
$ sudo dpkg-reconfigure openssh-server
After the system regenerated the SSH keys I was able to connect via successfully.