I've many different ssh keys in ~/.ssh, which I used happily through .ssh/config or -i option on Debian Lenny.
Recently I've installed Linux Debian Mint and I was no longer able to access some hosts. The reason was that ssh is offering all the keys in ~/.ssh without giving precedence to the specified key. So, ssh may disconnect for "Too many authentication failures" if the right key happens to be at the bottom of the list.
My workaround was to move most keys in another directory, and update .ssh/config and scripts accordingly.
It works but I'm not fully satisfied with it.