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The ability to specify the precise position on the screen you want
your PuTTY window to open at. This is clearly a very useful thing to
have, but it would be just as useful for all the other
Windows apps anyone uses. It shouldn't be the responsibility of
every single program to include a configuration option to specify
window position. Instead, it should be the responsibility of the
Windows system itself, or a third-party program, to remember where
you like individual programs to go.
One such program is WinSize (free, at least as in beer); another is ZMover (shareware); yet another is HandyThing (also shareware). If anyone knows of a free (as in speech) one, I'd like to hear about it.