Sorry, I haven't personally tried this one just yet, but because I am wanting this while bundling up an atom-shell app, I found it very interesting when https://github.com/atom/rcedit showed up in my first search for the RCEDIT utility mentioned in other answers.
One of its commands is:
$ rcedit "path-to-exe-or-dll" --set-icon "path-to-ico"
…so assuming this works, it is likely the solution I will use — my Windows build machine is already set up to fetch source using git
and compile via gyp
.
UPDATE: there's a pre-built executable available via https://github.com/atom/rcedit/releases/ and it works well for me on Win7 (from Git Bash/Msys shell although I'd be surprised if that makes a difference).