I've reach to this problem when trying to install composer on a Window 7 machine from http://getcomposer.org/download page. As there was an existing compose version (provided by acquia Dev Desktop tool) the installation fails and the only chance was to fix this issue manually. (or to remove Dev Desktop tool composer).
Anyway the error message is quite straightforward (Could not open input file: composer.phar), we should then tell the system where the file is located.
Edit composer.bat file and should look like:
@SET PATH=C:\Program Files (x86)\DevDesktop\php5_4;%PATH%
php.exe composer.phar %*
See that composer.phar doesn´t have a file path. When standing in a different folder than the one where composer.phar is located the system won´t be able to find it. So, just complete the composer.phar file path:
@SET PATH=C:\Program Files (x86)\DevDesktop\php5_4;;%PATH%
SET composerScript=composer.phar
php.exe "%~dp0%composerScript%" %*
Reopen your window console and that should do the trick.
EDIT: this has an issue because it always uses %~dp0%composerScript% folder as composer execution. Then all configurations are done in that folder (besides standing on your current project folder) and not in your project folder.
So far I haven't found a was to make a manual composer installation to work globally on Windows. Perhaps you should go ahead with composer for windows installation mentioned above.