Outputting a PNG graphic without margins or footer
Per the documentation at http://lilypond.org/doc/v2.18/Documentation/usage/lilypond-output-in-other-programs, the following options will output a nicely formatted PNG with no margins or footer:
lilypond -dbackend=eps -dno-gs-load-fonts -dinclude-eps-fonts --png myfile.ly
However, this assumes that you've disabled Lilypond's default tagline by adding tagline = ##f in the \header section
of your document, and that you haven't set any other footer elements such as copyright. It seems that if any footer content is present, it will be included in the png.
Possible workaround: declare a hidefooter scheme variable in the lilypond command line options, and define a custom scheme function that controls definition of footer elements based on whether hidefooter is ##t