After uploading my sketch to the Uno, I want to call a DOS batchfile which sends some special serial commands to it through a serial COM port. Is there any way to add an extra stage to the Arduino IDE build and upload process that runs automatically
Change the avrdude tool to your batch file. Run avrdude with the passed arguments from the batch file and then send your serial commands.
You may want to creating your own custom hardware package that references the arduino:arduino core so that you don't need to redo your changes every time you update to a new version of Arduino AVR Boards/Arduino IDE.