What my setup does is that I use JSBuilder to create a single file, and then use ycompressor to compress this js file.
Here is my batch file with one click, hope it works for you.
cd C:\wamp\www\sencha-touch-1.1.1\jsbuilder CALL JSBuilder.bat -v -p "C:\wamp\www\my-sencha-project\mobile_app_deploy.jsb3" -d "C:\wamp\www\my-sencha-project\" java -jar ycompressor\ycompressor.jar --charset utf8 -o C:\wamp\www\sencha-touch-1.1.1\jsbuilder\my-sencha-project-mini.js --nomunge C:\wamp\www\sencha-touch-1.1.1\jsbuilder\ybapp.js xcopy ybapp.js c:\wamp\www\my-sencha-project\js /y xcopy ybapp-mini.js c:\wamp\www\my-sencha-project\js\ /y pause
* my mobile_app_deploy.jsb3 contains the source sencha-touch.jsb3 file and also my own js files for my sencha application.
Hope this helps you and other readers.
(ps. maybe there should be a jsb3 tag)
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