I have a source file with two similar yet subtly different sections. I\'d like to merge the two sections into one subroutine with a parameter that handles the subtle difference
KDiff3 is open source and available on several platforms including Win32 and Linux.
It has the "manual alignment" feature discussed by Gishu about Beyond Compare (which by the way I haven't been using personally but is considered a great tool by many people I know).
See this answer for more examples.