As a counterpoint, I LOVE the whole ~/.ssh directory. It keeps everything in one place, is text-editable, is cross-platform between Mac and Linux, and easily transferred to new machines, or restored to existing ones after a fresh reinstall.

With Putty, if I want to change, say, the size of the terminal opened on connections, I'd have to update every Putty session individually. Been there; done that. Ridiculous. That should be a function of the terminal you run SSH under, not the SSH session itself.