I have been using APT (Aperture Photometry Tool) by Russ Laher for all my VS work. It is free, as in both speech and beer, and platform-neutral because it is wrotten in Java. Russ is on the IPAC team and has produced a very fine program. He is responsive to bug reports and feature requests, a few of which I have made.
APT produces output in its own TBL format (basically TSV with an initial couple of comment lines and another at the end) which it can export to CSV for loading into any standard spreadsheet. One nice feature of APT is that one FITS card can be exported into a CSV column — I use it to record for either JD or HJD according to what is desired for later analysis — as well as the complete FITS header where it is readily available for subsequent processing.
Converting the CSV into a BAA-VSS TSV-format file is easy enough and I will happily provide my script on request. The script uses ensemble photometry to produce an instrumental zero point magnitude from a list of (magnitude, error) pairs for the sequence members and then propagates errors appropriately to the derived magnitude of the VS.
I have another script which take an AAVSO VSP photometry web page and generates the correct source list and sequence data files for APT and the script noted above respectively. Naturally this script is also freely available.