How do I set the version information for an existing .exe, .dll?

While it's not a batch process, Visual Studio can also add/edit file resources.

Just use File->Open->File on the .EXE or .DLL. This is handy for fixing version information post-build, or adding it to files that don't have these resources to begin with.

Unlike many of the other answers, this solution uses completely free software.

Firstly, create a file called Resources.rc like this:

VS_VERSION_INFO VERSIONINFO
    FILEVERSION    1,0,0,0
    PRODUCTVERSION 1,0,0,0
{
    BLOCK "StringFileInfo"
    {
        BLOCK "040904b0"
        {
            VALUE "CompanyName",        "ACME Inc.\0"
            VALUE "FileDescription",    "MyProg\0"
            VALUE "FileVersion",        "1.0.0.0\0"
            VALUE "LegalCopyright",     "© 2013 ACME Inc. All Rights Reserved\0"
            VALUE "OriginalFilename",   "MyProg.exe\0"
            VALUE "ProductName",        "My Program\0"
            VALUE "ProductVersion",     "1.0.0.0\0"
        }
    }
    BLOCK "VarFileInfo"
    {
        VALUE "Translation", 0x409, 1200
    }
}

Next, use GoRC to compile it to a .res file using:

GoRC /fo Resources.res Resources.rc

^{(see my comment below for a mirror of GoRC.exe)}

Then use Resource Hacker in CLI mode to add it to an existing .exe:

ResHacker -add MyProg.exe, MyProg.exe, Resources.res,,,

That's it!

Or you could check out the freeware StampVer for Win32 exe/dll files.
It will only change the file and product versions though if they have a version resource already. It cannot add a version resource if one doesn’t exist.

rcedit is relative new and works well from the command line: https://github.com/atom/rcedit

$ rcedit "path-to-exe-or-dll" --set-version-string "Comments" "This is an exe"
$ rcedit "path-to-exe-or-dll" --set-file-version "10.7"
$ rcedit "path-to-exe-or-dll" --set-product-version "10.7"

There's also an NPM module which wraps it from JavaScript and a Grunt task in case you're using Grunt.

What about something like this?

verpatch /va foodll.dll %VERSION% %FILEDESCR% %COMPINFO% %PRODINFO% %BUILDINFO%

Available here with full sources.