Using git on Windows git comes bundled with its own ssh. This is properly fine for most people, however I personally preferer using the Putty tools. Being an active user of Bazaar (uses plink by default) and I already have my ssh-keys setup using Putty Pageant.
To change git to use plink (the command line version of putty) just the the following environment variable
GIT_SSH=C:\Program Files\PuTTY\plink.exe #Using powershell [Environment]::SetEnvironmentVariable("GIT_SSH", "C:\Program Files\PuTTY\plink.exe", "User")
Problem adding new host keys
For some unknown reason when using plink with git, It does not allow any keybord input, so you cant enter y to store the key.
The server's rsa2 key fingerprint is: <XXXXXXX> [...] Store key in cache? (y/n)
To workaround you can simply connect to the server using putty and add the hostkey by pressing yes. I’m guessing this is a bug and will be fixed in a future version of putty or git.