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Will Google penalise me for doing this?
They won't be links or anything.
A 1x1 image, whether invisible or not, is a valid design tool...a 1x1 invisible link can never be utilized by a real person and therefore is spam.
If you *do* use 1x1 GIFs for formatting purposes, using alt="" is the right thing to do (make sure they are not linked, though, or you may get into trouble with the SE).
However, unless you have to support *really* old browsers, using CSS for layout may be a better (and faster) solution.