For Git Bash

If you are running msysgit (I am assuming you are) and are looking to run Git Bash (I recommend it over TortoiseGit, but I lean to the CLI more than GUI now), you need to figure out what your home directory is for Git Bash by starting it then type pwd (On Windows 7, it will be something like C:\Users\phsr I think). While you're in Git Bash, you should mkdir .ssh.

After you have the home directory, and a .ssh folder under that, you want to open PuTTYgen and open the key (.ppk file) you have previously created. Once your key is open, you want to select Conversions -> Export OpenSSH key and save it to HOME\.ssh\id_rsa. After you have the key at that location, Git Bash will recognize the key and use it.

Note: Comments indicate that this doesn't work in all cases. You may need to copy the OpenSSH key to Program Files\Git\.ssh\id_rsa (or Program Files (x86)\Git\.ssh\id_rsa).

For TortoiseGit

When using TortoiseGit, you need to set the SSH key via pacey's directions. You need to do that for every repository you are using TortoiseGit with.

It looks like your connection is failing because the ssh host key of your target host has changed:

Host key verification failed.

Because of this error your ssh connection is failing. You need to either update the cached host key on your local system, or figure out why the host key on the remote system has changed. You can update your local key like this:

# ssh-keygen -R 161.3.46.12
# ssh root@161.3.46.12

This should prompt you to accept the new host key.

Do note that host key verification is a fatal error for a reason; it can mean that your remote server has been compromised. More often it means that someone has re-installed a system without preserving the host key.